6WIH

N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Structure of human mitochondrial complex Nfs1-ISCU2(L35H36)-ISD11 with E.coli ACP1 at 1.9 A resolution (NIAU)2.

PDB DOI: https://doi.org/10.2210/pdb6WIH/pdb

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

Deposited: 2020-04-09 Released: 2020-05-13
Deposition Author(s): Boniecki, M.T., Cygler, M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.186
R-Value Work: 0.151
R-Value Observed: 0.152

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: 86.19 kDa
Atom Count: 6,188
Modelled Residue Count: 685
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): 1 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 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Q1 Query on 8Q1 Download Ideal Coordinates CCD File SDF format, chain FB [auth C] MOL2 format, chain FB [auth C] mmCIF format, chain FB [auth C]	FB [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 FB [auth C] Interactions & Density Focus chain FB [auth C]
P15 Query on P15 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
EDT Query on EDT Download Ideal Coordinates CCD File SDF format, chain EB [auth B] MOL2 format, chain EB [auth B] mmCIF format, chain EB [auth B]	EB [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain EB [auth B] Interactions & Density Focus chain EB [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 KB [auth D] MOL2 format, chain KB [auth D] mmCIF format, chain KB [auth D]	KB [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain KB [auth D] Interactions & Density Focus chain KB [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	U [auth A], V [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain U [auth A] Focus chain V [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A]	FA [auth A], NA [auth A], OA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain NA [auth A] Focus chain OA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain T [auth A] SDF format, chain W [auth A] SDF format, chain YA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth B]	AB [auth B] BA [auth A] EA [auth A] F [auth A] RA [auth A] AB [auth B], BA [auth A], EA [auth A], F [auth A], RA [auth A], SA [auth A], T [auth A], W [auth A], YA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain W [auth A] Focus chain YA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain W [auth A] Focus chain YA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain MB [auth D] SDF format, chain VA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain VA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain VA [auth B]	G [auth A], H [auth A], I [auth A], MB [auth D], VA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MB [auth D] Focus chain VA [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MB [auth D] Focus chain VA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth C] SDF format, chain HA [auth A] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain IB [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth B] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	BB [auth B] CA [auth A] CB [auth B] DA [auth A] DB [auth B] BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], J [auth A], JA [auth A], JB [auth D], K [auth A], KA [auth A], L [auth A], LA [auth A], LB [auth D], M [auth A], MA [auth A], N [auth A], NB [auth D], O [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], S [auth A], TA [auth A], UA [auth B], WA [auth B], X [auth A], XA [auth B], Y [auth A], Z [auth A], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B]