7RTK | pdb_00007rtk

Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb7RTK/pdb

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

Deposited: 2021-08-13 Released: 2021-08-25
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: 2.50 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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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: 85.53 kDa
Atom Count: 5,798
Modeled Residue Count: 678
Deposited Residue Count: 717
Unique protein chains: 4

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y697
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HD34
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C	77	Escherichia coli	Mutation(s): 0 Gene Names: acpP, ECS88_1108
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8 Go to UniProtKB: P0A6A8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6A8
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 VA [auth C] MOL2 format, chain VA [auth C] mmCIF format, chain VA [auth C]	VA [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 VA [auth C] Interactions & Density Focus chain VA [auth C]
P15 Query on P15 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
EDT Query on EDT Download:Ideal Coordinates CCD File SDF format, chain UA [auth B] MOL2 format, chain UA [auth B] mmCIF format, chain UA [auth B]	UA [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain UA [auth B] Interactions & Density Focus chain UA [auth B]
PLP (Subject of Investigation/LOI) 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 ZA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain ZA [auth D]	ZA [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain ZA [auth D] Interactions & Density Focus chain ZA [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] MOL2 format, chain WA [auth C] mmCIF format, chain WA [auth C]	WA [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain WA [auth C] Interactions & Density Focus chain WA [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
DTT Query on DTT 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]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A]	BA [auth A], FA [auth A], GA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain BA [auth A] Focus chain FA [auth A] Focus chain GA [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain RA [auth B] SDF format, chain U [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	KA [auth A] LA [auth A] OA [auth B] PA [auth B] RA [auth B] KA [auth A], LA [auth A], OA [auth B], PA [auth B], RA [auth B], U [auth A], Y [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain KA [auth A] Focus chain LA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain U [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain U [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	BB [auth D], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain BB [auth D] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain XA [auth C] SDF format, chain YA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth D]	AB [auth D] CA [auth A] CB [auth D] DA [auth A] EA [auth A] AB [auth D], CA [auth A], CB [auth D], DA [auth A], EA [auth A], F [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], L [auth A], M [auth A], MA [auth A], N [auth A], NA [auth B], O [auth A], P [auth A], Q [auth A], QA [auth B], R [auth A], S [auth A], SA [auth B], TA [auth B], V [auth A], W [auth A], XA [auth C], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth C] Focus chain YA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth C] Focus chain YA [auth D]