7COH

Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State

PDB DOI: https://doi.org/10.2210/pdb7COH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Expression System: Bos taurus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2020-08-04 Released: 2021-04-07
Deposition Author(s): Shinzawa-Itoh, K., Muramoto, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.170 (Depositor), 0.180 (DCC)
R-Value Work:
0.148 (Depositor), 0.160 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1occ 2occ 1v54 2dyr 5b1a

Literature

The 1.3-A Resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism

Shinzawa-Itoh, K., Hatanaka, M., Fujita, K., Yano, N., Ogasawara, Y., Iwata, J., Yamashita, E., Tsukihara, T., Yoshikawa, S., Muramoto, K.

(2021) Biochim Biophys Acta

DOI: https://doi.org/10.1016/j.bbadva.2021.100009

Macromolecule Content

Total Structure Weight: 460.73 kDa
Atom Count: 33,049
Modelled Residue Count: 3,474
Deposited Residue Count: 3,614
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 Gene Names: MT-CO1, COI, COXI, MTCO1 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00396
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68530
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	261	Bos taurus	Mutation(s): 0 Gene Names: MT-CO3, COIII, COXIII, MTCO3 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
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UniProt Group	P00415
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1	D, Q	147	Bos taurus	Mutation(s): 0 Gene Names: COX4I1, COX4 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
Entity Groups
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UniProt Group	P00423
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A	E, R	109	Bos taurus	Mutation(s): 0 Gene Names: COX5A Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
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UniProt Group	P00426
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B	F, S	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
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UniProt Group	P00428
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	G, T	85	Bos taurus	Mutation(s): 0 Gene Names: COX6A2, COX6A Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
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UniProt Group	P07471
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	85	Bos taurus	Mutation(s): 0 Gene Names: COX6B1, COX6B Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
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UniProt Group	P00429
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Gene Names: COX6C Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
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UniProt Group	P04038
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1	J, W	59	Bos taurus	Mutation(s): 0 Gene Names: COX7A1, COX7A, COX7AH Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
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UniProt Group	P07470
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B	K, X	56	Bos taurus	Mutation(s): 0 Gene Names: COX7B Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
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UniProt Group	P13183
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	47	Bos taurus	Mutation(s): 0 Gene Names: COX7C, COX7CP1 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
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UniProt Group	P00430
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B	M, Z	46	Bos taurus	Mutation(s): 0 Gene Names: COX8B, COX8H Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
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UniProt Group	P10175
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Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain JE [auth P] SDF format, chain TC [auth N] SDF format, chain UB [auth C] SDF format, chain UC [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain JE [auth P] MOL2 format, chain TC [auth N] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain JE [auth P] mmCIF format, chain TC [auth N] mmCIF format, chain UB [auth C] mmCIF format, chain UC [auth N]	FA [auth A] GA [auth A] JE [auth P] TC [auth N] UB [auth C] FA [auth A], GA [auth A], JE [auth P], TC [auth N], UB [auth C], UC [auth N]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain FA [auth A] Focus chain GA [auth A] Focus chain JE [auth P] Focus chain TC [auth N] Focus chain UB [auth C] Focus chain UC [auth N] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth A] Focus chain JE [auth P] Focus chain TC [auth N] Focus chain UB [auth C] Focus chain UC [auth N]
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain OC [auth N] SDF format, chain PC [auth N] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain OC [auth N] MOL2 format, chain PC [auth N] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain OC [auth N] mmCIF format, chain PC [auth N]	AA [auth A], BA [auth A], OC [auth N], PC [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain OC [auth N] Focus chain PC [auth N] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain OC [auth N] Focus chain PC [auth N]
PEK (Subject of Investigation/LOI) Query on PEK Download Ideal Coordinates CCD File SDF format, chain GE [auth P] SDF format, chain RB [auth C] MOL2 format, chain GE [auth P] MOL2 format, chain RB [auth C] mmCIF format, chain GE [auth P] mmCIF format, chain RB [auth C]	GE [auth P], RB [auth C]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C₄₃ H₇₈ N O₈ P ANRKEHNWXKCXDB-BHFWLYLHSA-N		Interactions Focus chain GE [auth P] Focus chain RB [auth C] Interactions & Density Focus chain GE [auth P] Focus chain RB [auth C]
PGV (Subject of Investigation/LOI) Query on PGV Download Ideal Coordinates CCD File SDF format, chain HE [auth P] SDF format, chain IE [auth P] SDF format, chain SB [auth C] SDF format, chain TB [auth C] MOL2 format, chain HE [auth P] MOL2 format, chain IE [auth P] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth C] mmCIF format, chain HE [auth P] mmCIF format, chain IE [auth P] mmCIF format, chain SB [auth C] mmCIF format, chain TB [auth C]	HE [auth P], IE [auth P], SB [auth C], TB [auth C]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain HE [auth P] Focus chain IE [auth P] Focus chain SB [auth C] Focus chain TB [auth C] Interactions & Density Focus chain HE [auth P] Focus chain IE [auth P] Focus chain SB [auth C] Focus chain TB [auth C]
DMU (Subject of Investigation/LOI) Query on DMU Download Ideal Coordinates CCD File SDF format, chain AD [auth N] SDF format, chain AE [auth P] SDF format, chain AF [auth W] SDF format, chain BD [auth N] SDF format, chain BE [auth P] SDF format, chain BF [auth Y] SDF format, chain CD [auth N] SDF format, chain CF [auth Z] SDF format, chain FC [auth G] SDF format, chain GB [auth C] SDF format, chain GC [auth G] SDF format, chain HB [auth C] SDF format, chain HC [auth G] SDF format, chain IA [auth A] SDF format, chain ID [auth O] SDF format, chain JB [auth C] SDF format, chain JD [auth O] SDF format, chain KB [auth C] SDF format, chain KC [auth J] SDF format, chain KD [auth O] SDF format, chain LB [auth C] SDF format, chain LC [auth J] SDF format, chain LE [auth P] SDF format, chain MA [auth A] SDF format, chain MB [auth C] SDF format, chain MC [auth L] SDF format, chain NA [auth A] SDF format, chain NC [auth M] SDF format, chain OA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain UE [auth T] SDF format, chain VA [auth B] SDF format, chain VD [auth P] SDF format, chain VE [auth T] SDF format, chain WB [auth C] SDF format, chain WC [auth N] SDF format, chain WD [auth P] SDF format, chain WE [auth T] SDF format, chain YD [auth P] SDF format, chain ZD [auth P] SDF format, chain ZE [auth W] MOL2 format, chain AD [auth N] MOL2 format, chain AE [auth P] MOL2 format, chain AF [auth W] MOL2 format, chain BD [auth N] MOL2 format, chain BE [auth P] MOL2 format, chain BF [auth Y] MOL2 format, chain CD [auth N] MOL2 format, chain CF [auth Z] MOL2 format, chain FC [auth G] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth G] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth G] MOL2 format, chain IA [auth A] MOL2 format, chain ID [auth O] MOL2 format, chain JB [auth C] MOL2 format, chain JD [auth O] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth J] MOL2 format, chain KD [auth O] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth J] MOL2 format, chain LE [auth P] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth L] MOL2 format, chain NA [auth A] MOL2 format, chain NC [auth M] MOL2 format, chain OA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain UE [auth T] MOL2 format, chain VA [auth B] MOL2 format, chain VD [auth P] MOL2 format, chain VE [auth T] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth N] MOL2 format, chain WD [auth P] MOL2 format, chain WE [auth T] MOL2 format, chain YD [auth P] MOL2 format, chain ZD [auth P] MOL2 format, chain ZE [auth W] mmCIF format, chain AD [auth N] mmCIF format, chain AE [auth P] mmCIF format, chain AF [auth W] mmCIF format, chain BD [auth N] mmCIF format, chain BE [auth P] mmCIF format, chain BF [auth Y] mmCIF format, chain CD [auth N] mmCIF format, chain CF [auth Z] mmCIF format, chain FC [auth G] mmCIF format, chain GB [auth C] mmCIF format, chain GC [auth G] mmCIF format, chain HB [auth C] mmCIF format, chain HC [auth G] mmCIF format, chain IA [auth A] mmCIF format, chain ID [auth O] mmCIF format, chain JB [auth C] mmCIF format, chain JD [auth O] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth J] mmCIF format, chain KD [auth O] mmCIF format, chain LB [auth C] mmCIF format, chain LC [auth J] mmCIF format, chain LE [auth P] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth L] mmCIF format, chain NA [auth A] mmCIF format, chain NC [auth M] mmCIF format, chain OA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain UE [auth T] mmCIF format, chain VA [auth B] mmCIF format, chain VD [auth P] mmCIF format, chain VE [auth T] mmCIF format, chain WB [auth C] mmCIF format, chain WC [auth N] mmCIF format, chain WD [auth P] mmCIF format, chain WE [auth T] mmCIF format, chain YD [auth P] mmCIF format, chain ZD [auth P] mmCIF format, chain ZE [auth W]	AD [auth N] AE [auth P] AF [auth W] BD [auth N] BE [auth P] AD [auth N], AE [auth P], AF [auth W], BD [auth N], BE [auth P], BF [auth Y], CD [auth N], CF [auth Z], FC [auth G], GB [auth C], GC [auth G], HB [auth C], HC [auth G], IA [auth A], ID [auth O], JB [auth C], JD [auth O], KB [auth C], KC [auth J], KD [auth O], LB [auth C], LC [auth J], LE [auth P], MA [auth A], MB [auth C], MC [auth L], NA [auth A], NC [auth M], OA [auth A], TA [auth B], UA [auth B], UE [auth T], VA [auth B], VD [auth P], VE [auth T], WB [auth C], WC [auth N], WD [auth P], WE [auth T], YD [auth P], ZD [auth P], ZE [auth W]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain AD [auth N] Focus chain AE [auth P] Focus chain AF [auth W] Focus chain BD [auth N] Focus chain BE [auth P] Focus chain BF [auth Y] Focus chain CD [auth N] Focus chain CF [auth Z] Focus chain FC [auth G] Focus chain GB [auth C] Focus chain GC [auth G] Focus chain HB [auth C] Focus chain HC [auth G] Focus chain IA [auth A] Focus chain ID [auth O] Focus chain JB [auth C] Focus chain JD [auth O] Focus chain KB [auth C] Focus chain KC [auth J] Focus chain KD [auth O] Focus chain LB [auth C] Focus chain LC [auth J] Focus chain LE [auth P] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain MC [auth L] Focus chain NA [auth A] Focus chain NC [auth M] Focus chain OA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain UE [auth T] Focus chain VA [auth B] Focus chain VD [auth P] Focus chain VE [auth T] Focus chain WB [auth C] Focus chain WC [auth N] Focus chain WD [auth P] Focus chain WE [auth T] Focus chain YD [auth P] Focus chain ZD [auth P] Focus chain ZE [auth W] Interactions & Density Focus chain AD [auth N] Focus chain AE [auth P] Focus chain AF [auth W] Focus chain BD [auth N] Focus chain BE [auth P] Focus chain BF [auth Y] Focus chain CD [auth N] Focus chain CF [auth Z] Focus chain FC [auth G] Focus chain GB [auth C] Focus chain GC [auth G] Focus chain HB [auth C] Focus chain HC [auth G] Focus chain IA [auth A] Focus chain ID [auth O] Focus chain JB [auth C] Focus chain JD [auth O] Focus chain KB [auth C] Focus chain KC [auth J] Focus chain KD [auth O] Focus chain LB [auth C] Focus chain LC [auth J] Focus chain LE [auth P] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain MC [auth L] Focus chain NA [auth A] Focus chain NC [auth M] Focus chain OA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain UE [auth T] Focus chain VA [auth B] Focus chain VD [auth P] Focus chain VE [auth T] Focus chain WB [auth C] Focus chain WC [auth N] Focus chain WD [auth P] Focus chain WE [auth T] Focus chain YD [auth P] Focus chain ZD [auth P] Focus chain ZE [auth W]
CHD (Subject of Investigation/LOI) Query on CHD Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain JC [auth G] SDF format, chain KE [auth P] SDF format, chain VB [auth C] SDF format, chain VC [auth N] SDF format, chain YE [auth T] MOL2 format, chain HA [auth A] MOL2 format, chain JC [auth G] MOL2 format, chain KE [auth P] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth N] MOL2 format, chain YE [auth T] mmCIF format, chain HA [auth A] mmCIF format, chain JC [auth G] mmCIF format, chain KE [auth P] mmCIF format, chain VB [auth C] mmCIF format, chain VC [auth N] mmCIF format, chain YE [auth T]	HA [auth A] JC [auth G] KE [auth P] VB [auth C] VC [auth N] HA [auth A], JC [auth G], KE [auth P], VB [auth C], VC [auth N], YE [auth T]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain HA [auth A] Focus chain JC [auth G] Focus chain KE [auth P] Focus chain VB [auth C] Focus chain VC [auth N] Focus chain YE [auth T] Interactions & Density Focus chain HA [auth A] Focus chain JC [auth G] Focus chain KE [auth P] Focus chain VB [auth C] Focus chain VC [auth N] Focus chain YE [auth T]
LFA (Subject of Investigation/LOI) Query on LFA Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain DC [auth G] SDF format, chain EB [auth C] SDF format, chain EC [auth G] SDF format, chain FB [auth C] SDF format, chain IB [auth C] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain ND [auth P] SDF format, chain OD [auth P] SDF format, chain PD [auth P] SDF format, chain QD [auth P] SDF format, chain RD [auth P] SDF format, chain SD [auth P] SDF format, chain SE [auth T] SDF format, chain TD [auth P] SDF format, chain TE [auth T] SDF format, chain UD [auth P] SDF format, chain XD [auth P] SDF format, chain YA [auth C] SDF format, chain YC [auth N] SDF format, chain ZA [auth C] SDF format, chain ZC [auth N] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth G] MOL2 format, chain EB [auth C] MOL2 format, chain EC [auth G] MOL2 format, chain FB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain ND [auth P] MOL2 format, chain OD [auth P] MOL2 format, chain PD [auth P] MOL2 format, chain QD [auth P] MOL2 format, chain RD [auth P] MOL2 format, chain SD [auth P] MOL2 format, chain SE [auth T] MOL2 format, chain TD [auth P] MOL2 format, chain TE [auth T] MOL2 format, chain UD [auth P] MOL2 format, chain XD [auth P] MOL2 format, chain YA [auth C] MOL2 format, chain YC [auth N] MOL2 format, chain ZA [auth C] MOL2 format, chain ZC [auth N] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth G] mmCIF format, chain EB [auth C] mmCIF format, chain EC [auth G] mmCIF format, chain FB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain ND [auth P] mmCIF format, chain OD [auth P] mmCIF format, chain PD [auth P] mmCIF format, chain QD [auth P] mmCIF format, chain RD [auth P] mmCIF format, chain SD [auth P] mmCIF format, chain SE [auth T] mmCIF format, chain TD [auth P] mmCIF format, chain TE [auth T] mmCIF format, chain UD [auth P] mmCIF format, chain XD [auth P] mmCIF format, chain YA [auth C] mmCIF format, chain YC [auth N] mmCIF format, chain ZA [auth C] mmCIF format, chain ZC [auth N]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] DC [auth G] AB [auth C], BB [auth C], CB [auth C], DB [auth C], DC [auth G], EB [auth C], EC [auth G], FB [auth C], IB [auth C], KA [auth A], LA [auth A], ND [auth P], OD [auth P], PD [auth P], QD [auth P], RD [auth P], SD [auth P], SE [auth T], TD [auth P], TE [auth T], UD [auth P], XD [auth P], YA [auth C], YC [auth N], ZA [auth C], ZC [auth N]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain DC [auth G] Focus chain EB [auth C] Focus chain EC [auth G] Focus chain FB [auth C] Focus chain IB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain ND [auth P] Focus chain OD [auth P] Focus chain PD [auth P] Focus chain QD [auth P] Focus chain RD [auth P] Focus chain SD [auth P] Focus chain SE [auth T] Focus chain TD [auth P] Focus chain TE [auth T] Focus chain UD [auth P] Focus chain XD [auth P] Focus chain YA [auth C] Focus chain YC [auth N] Focus chain ZA [auth C] Focus chain ZC [auth N] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain DC [auth G] Focus chain EB [auth C] Focus chain EC [auth G] Focus chain FB [auth C] Focus chain IB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain ND [auth P] Focus chain OD [auth P] Focus chain PD [auth P] Focus chain QD [auth P] Focus chain RD [auth P] Focus chain SD [auth P] Focus chain SE [auth T] Focus chain TD [auth P] Focus chain TE [auth T] Focus chain UD [auth P] Focus chain XD [auth P] Focus chain YA [auth C] Focus chain YC [auth N] Focus chain ZA [auth C] Focus chain ZC [auth N]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain MD [auth O] SDF format, chain XA [auth B] MOL2 format, chain MD [auth O] MOL2 format, chain XA [auth B] mmCIF format, chain MD [auth O] mmCIF format, chain XA [auth B]	MD [auth O], XA [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain MD [auth O] Focus chain XA [auth B] Interactions & Density Focus chain MD [auth O] Focus chain XA [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CC [auth F] SDF format, chain RE [auth S] MOL2 format, chain CC [auth F] MOL2 format, chain RE [auth S] mmCIF format, chain CC [auth F] mmCIF format, chain RE [auth S]	CC [auth F], RE [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CC [auth F] Focus chain RE [auth S] Interactions & Density Focus chain CC [auth F] Focus chain RE [auth S]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain QC [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain QC [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain QC [auth N]	CA [auth A], QC [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain QC [auth N] Interactions & Density Focus chain CA [auth A] Focus chain QC [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AC [auth F] SDF format, chain BC [auth F] SDF format, chain CE [auth P] SDF format, chain DD [auth N] SDF format, chain DE [auth P] SDF format, chain ED [auth N] SDF format, chain EE [auth P] SDF format, chain FD [auth N] SDF format, chain GD [auth N] SDF format, chain HD [auth N] SDF format, chain IC [auth G] SDF format, chain LD [auth O] SDF format, chain ME [auth R] SDF format, chain NB [auth C] SDF format, chain NE [auth R] SDF format, chain OB [auth C] SDF format, chain OE [auth R] SDF format, chain PA [auth A] SDF format, chain PB [auth C] SDF format, chain PE [auth S] SDF format, chain QA [auth A] SDF format, chain QE [auth S] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain WA [auth B] SDF format, chain XB [auth E] SDF format, chain XE [auth T] SDF format, chain YB [auth E] SDF format, chain ZB [auth E] MOL2 format, chain AC [auth F] MOL2 format, chain BC [auth F] MOL2 format, chain CE [auth P] MOL2 format, chain DD [auth N] MOL2 format, chain DE [auth P] MOL2 format, chain ED [auth N] MOL2 format, chain EE [auth P] MOL2 format, chain FD [auth N] MOL2 format, chain GD [auth N] MOL2 format, chain HD [auth N] MOL2 format, chain IC [auth G] MOL2 format, chain LD [auth O] MOL2 format, chain ME [auth R] MOL2 format, chain NB [auth C] MOL2 format, chain NE [auth R] MOL2 format, chain OB [auth C] MOL2 format, chain OE [auth R] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain PE [auth S] MOL2 format, chain QA [auth A] MOL2 format, chain QE [auth S] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain XB [auth E] MOL2 format, chain XE [auth T] MOL2 format, chain YB [auth E] MOL2 format, chain ZB [auth E] mmCIF format, chain AC [auth F] mmCIF format, chain BC [auth F] mmCIF format, chain CE [auth P] mmCIF format, chain DD [auth N] mmCIF format, chain DE [auth P] mmCIF format, chain ED [auth N] mmCIF format, chain EE [auth P] mmCIF format, chain FD [auth N] mmCIF format, chain GD [auth N] mmCIF format, chain HD [auth N] mmCIF format, chain IC [auth G] mmCIF format, chain LD [auth O] mmCIF format, chain ME [auth R] mmCIF format, chain NB [auth C] mmCIF format, chain NE [auth R] mmCIF format, chain OB [auth C] mmCIF format, chain OE [auth R] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain PE [auth S] mmCIF format, chain QA [auth A] mmCIF format, chain QE [auth S] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain XB [auth E] mmCIF format, chain XE [auth T] mmCIF format, chain YB [auth E] mmCIF format, chain ZB [auth E]	AC [auth F] BC [auth F] CE [auth P] DD [auth N] DE [auth P] AC [auth F], BC [auth F], CE [auth P], DD [auth N], DE [auth P], ED [auth N], EE [auth P], FD [auth N], GD [auth N], HD [auth N], IC [auth G], LD [auth O], ME [auth R], NB [auth C], NE [auth R], OB [auth C], OE [auth R], PA [auth A], PB [auth C], PE [auth S], QA [auth A], QE [auth S], RA [auth A], SA [auth A], WA [auth B], XB [auth E], XE [auth T], YB [auth E], ZB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth F] Focus chain BC [auth F] Focus chain CE [auth P] Focus chain DD [auth N] Focus chain DE [auth P] Focus chain ED [auth N] Focus chain EE [auth P] Focus chain FD [auth N] Focus chain GD [auth N] Focus chain HD [auth N] Focus chain IC [auth G] Focus chain LD [auth O] Focus chain ME [auth R] Focus chain NB [auth C] Focus chain NE [auth R] Focus chain OB [auth C] Focus chain OE [auth R] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain PE [auth S] Focus chain QA [auth A] Focus chain QE [auth S] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain WA [auth B] Focus chain XB [auth E] Focus chain XE [auth T] Focus chain YB [auth E] Focus chain ZB [auth E] Interactions & Density Focus chain AC [auth F] Focus chain BC [auth F] Focus chain CE [auth P] Focus chain DD [auth N] Focus chain DE [auth P] Focus chain ED [auth N] Focus chain EE [auth P] Focus chain FD [auth N] Focus chain GD [auth N] Focus chain HD [auth N] Focus chain IC [auth G] Focus chain LD [auth O] Focus chain ME [auth R] Focus chain NB [auth C] Focus chain NE [auth R] Focus chain OB [auth C] Focus chain OE [auth R] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain PE [auth S] Focus chain QA [auth A] Focus chain QE [auth S] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain WA [auth B] Focus chain XB [auth E] Focus chain XE [auth T] Focus chain YB [auth E] Focus chain ZB [auth E]
PER Query on PER Download Ideal Coordinates CCD File SDF format, chain JA [auth A] SDF format, chain XC [auth N] MOL2 format, chain JA [auth A] MOL2 format, chain XC [auth N] mmCIF format, chain JA [auth A] mmCIF format, chain XC [auth N]	JA [auth A], XC [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain JA [auth A] Focus chain XC [auth N] Interactions & Density Focus chain JA [auth A] Focus chain XC [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain RC [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain RC [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain RC [auth N]	DA [auth A], RC [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain RC [auth N] Interactions & Density Focus chain DA [auth A] Focus chain RC [auth N]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain SC [auth N] MOL2 format, chain EA [auth A] MOL2 format, chain SC [auth N] mmCIF format, chain EA [auth A] mmCIF format, chain SC [auth N]	EA [auth A], SC [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain SC [auth N] Interactions & Density Focus chain EA [auth A] Focus chain SC [auth N]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain FE [auth P] SDF format, chain QB [auth C] MOL2 format, chain FE [auth P] MOL2 format, chain QB [auth C] mmCIF format, chain FE [auth P] mmCIF format, chain QB [auth C]	FE [auth P], QB [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain FE [auth P] Focus chain QB [auth C] Interactions & Density Focus chain FE [auth P] Focus chain QB [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A, N	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.170 (Depositor), 0.180 (DCC)
R-Value Work: 0.148 (Depositor), 0.160 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.998	α = 90
b = 204.193	β = 90
c = 177.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Shinzawa-Itoh, K.

Muramoto, K.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP17H03646
Japan Society for the Promotion of Science (JSPS)	Japan	JP22370060
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06162

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Deposit Data

Help and Resources

7COH

Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State

The 1.3-A Resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism

Entity ID: 1

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

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