8DHK | pdb_00008dhk

Crystal structure of human Sulfide Quinone Oxidoreductase K207E

PDB DOI: https://doi.org/10.2210/pdb8DHK/pdb

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

Deposited: 2022-06-27 Released: 2023-07-19
Deposition Author(s): Mascarenhas, R.N., Ludlum, A., Banerjee, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.237 (Depositor), 0.227 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Sulfide oxidation in human sulfide quinone oxidoreductase is enthalpically driven: Contributions of the Lys-207 general base

Bonanata, J., Landry, A., Ceric, K., Ludlam, A., Mascarenhas, R., Coitino, L., Banerjee, R.

To be published.

Macromolecule Content

Total Structure Weight: 97.51 kDa
Atom Count: 6,751
Modeled Residue Count: 811
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfide:quinone oxidoreductase	A, B	418	Homo sapiens	Mutation(s): 1 EC: 1.8.5.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6N5 (Homo sapiens) Explore Q9Y6N5 Go to UniProtKB: Q9Y6N5
PHAROS: Q9Y6N5 GTEx: ENSG00000137767
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
MHA Query on MHA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain E [auth A]	E [auth A], Q [auth B]	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID C₆ H₁₀ N₂ O₅ QZTKDVCDBIDYMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain Q [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] F [auth A] G [auth A] I [auth A] J [auth A] D [auth A], F [auth A], G [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain H [auth A]	H [auth A], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]