6W1D

Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2

PDB DOI: https://doi.org/10.2210/pdb6W1D/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-04 Released: 2020-03-18
Deposition Author(s): Boniecki, M.T., Cygler, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.189
R-Value Work: 0.159
R-Value Observed: 0.160

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis

Freibert, S.A., Boniecki, M.T., Shulz, V., Wilbrecht, C., Krapoth, N., Muhlenhoff, U., Stehling, O., Cygler, M., Lill, R.

To be published.

Macromolecule Content

Total Structure Weight: 87.55 kDa
Atom Count: 6,266
Modelled Residue Count: 680
Deposited Residue Count: 717
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase, mitochondrial	A	406	Homo sapiens	Mutation(s): 0 Gene Names: NFS1, NIFS, HUSSY-08 EC: 2.8.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y697 (Homo sapiens) Explore Q9Y697 Go to UniProtKB: Q9Y697
PHAROS: Q9Y697 GTEx: ENSG00000244005
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y697
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYR motif-containing protein 4	B	91	Homo sapiens	Mutation(s): 1 Gene Names: LYRM4, C6orf149, ISD11, CGI-203
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD34 (Homo sapiens) Explore Q9HD34 Go to UniProtKB: Q9HD34
PHAROS: Q9HD34 GTEx: ENSG00000214113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HD34
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C	77	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8 Go to UniProtKB: P0A6A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6A8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	D	143	Homo sapiens	Mutation(s): 0 Gene Names: ISCU, NIFUN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens) Explore Q9H1K1 Go to UniProtKB: Q9H1K1
PHAROS: Q9H1K1 GTEx: ENSG00000136003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Q1 Query on 8Q1 Download Ideal Coordinates CCD File SDF format, chain RB [auth C] MOL2 format, chain RB [auth C] mmCIF format, chain RB [auth C]	RB [auth C]	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate C₂₃ H₄₅ N₂ O₈ P S MVHUOSAYFQKAMT-NRFANRHFSA-N		Interactions Focus chain RB [auth C] Interactions & Density Focus chain RB [auth C]
P15 Query on P15 Download Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]
EDT Query on EDT Download Ideal Coordinates CCD File SDF format, chain NB [auth B] MOL2 format, chain NB [auth B] mmCIF format, chain NB [auth B]	NB [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain NB [auth B] Interactions & Density Focus chain NB [auth B]
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain YB [auth D] MOL2 format, chain YB [auth D] mmCIF format, chain YB [auth D]	YB [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain YB [auth D] Interactions & Density Focus chain YB [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain SB [auth C] MOL2 format, chain SB [auth C] mmCIF format, chain SB [auth C]	SB [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain SB [auth C] Interactions & Density Focus chain SB [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	W [auth A], X [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]
DTT Query on DTT Download Ideal Coordinates CCD File SDF format, chain KA [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain KA [auth A]	KA [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain KA [auth A] Interactions & Density Focus chain KA [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A]	LA [auth A], UA [auth A], VA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Interactions & Density Focus chain LA [auth A] Focus chain UA [auth A] Focus chain VA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BB [auth A] SDF format, chain EA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain LB [auth B] SDF format, chain V [auth A] SDF format, chain VB [auth C] SDF format, chain Y [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain ZA [auth A]	AB [auth A] BB [auth A] EA [auth A] IA [auth A] JA [auth A] AB [auth A], BB [auth A], EA [auth A], IA [auth A], JA [auth A], JB [auth B], LB [auth B], V [auth A], VB [auth C], Y [auth A], ZA [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain EA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain LB [auth B] Focus chain V [auth A] Focus chain VB [auth C] Focus chain Y [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain EA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain LB [auth B] Focus chain V [auth A] Focus chain VB [auth C] Focus chain Y [auth A] Focus chain ZA [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain CB [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain AC [auth D] MOL2 format, chain CB [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain AC [auth D] mmCIF format, chain CB [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	AC [auth D] CB [auth A] F [auth A] G [auth A] H [auth A] AC [auth D], CB [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain CB [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain AC [auth D] Focus chain CB [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain CC [auth D] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain P [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain U [auth A] SDF format, chain UB [auth C] SDF format, chain WA [auth A] SDF format, chain WB [auth C] SDF format, chain XA [auth A] SDF format, chain XB [auth D] SDF format, chain YA [auth A] SDF format, chain Z [auth A] SDF format, chain ZB [auth D] SDF format, chain BC [auth D] SDF format, chain PA [auth A] SDF format, chain TB [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth D] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth C] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth C] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain BC [auth D] MOL2 format, chain PA [auth A] MOL2 format, chain TB [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CC [auth D] mmCIF format, chain DB [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth C] mmCIF format, chain WA [auth A] mmCIF format, chain WB [auth C] mmCIF format, chain XA [auth A] mmCIF format, chain XB [auth D] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain BC [auth D] mmCIF format, chain PA [auth A] mmCIF format, chain TB [auth C]	AA [auth A] BA [auth A] BC [auth D] CA [auth A] CC [auth D] AA [auth A], BA [auth A], BC [auth D], CA [auth A], CC [auth D], DB [auth A], EB [auth A], FA [auth A], FB [auth A], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IB [auth B], J [auth A], K [auth A], KB [auth B], L [auth A], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], O [auth A], OA [auth A], OB [auth B], P [auth A], PA [auth A], PB [auth B], Q [auth A], QA [auth A], QB [auth B], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], TB [auth C], U [auth A], UB [auth C], WA [auth A], WB [auth C], XA [auth A], XB [auth D], YA [auth A], Z [auth A], ZB [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CC [auth D] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UB [auth C] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain XA [auth A] Focus chain XB [auth D] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CC [auth D] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UB [auth C] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain XA [auth A] Focus chain XB [auth D] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZB [auth D]