9QM0 | pdb_00009qm0

W-formate dehydrogenase U192C from Desulfovibrio vulgaris

PDB DOI: https://doi.org/10.2210/pdb9QM0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): Yes

Deposited: 2025-03-21 Released: 2025-07-16
Deposition Author(s): Vilela-Alves, G., Oliveira, A.R., Pereira, I.C., Romao, M.J., Mota, C.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.172 (Depositor), 0.182 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The Role of Selenocysteine in Catalysis and Oxygen Tolerance of a W‐Dependent Formate Dehydrogenase

Oliveira, A.R., Vilela-Alves, G., Mota, C., Fourmond, V., Leger, C., Biaso, F., Guigliarelli, B., Romao, M.J., Pereira, I.C.

(2025) ACS Catal

DOI: https://doi.org/10.1021/acscatal.5c02382

Macromolecule Content

Total Structure Weight: 141.15 kDa
Atom Count: 9,945
Modeled Residue Count: 1,184
Deposited Residue Count: 1,227
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, alpha subunit, selenocysteine-containing	A	1,013	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1 Gene Names: fdnG-1, DVU_0587 EC: 1.2.1.2
UniProt
Find proteins for Q72EJ1 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ1 Go to UniProtKB: Q72EJ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72EJ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, beta subunit, putative	B	214	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 Gene Names: DVU_0588
UniProt
Find proteins for Q72EJ0 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ0 Go to UniProtKB: Q72EJ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72EJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD (Subject of Investigation/LOI) Query on MGD 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]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain Y [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain Y [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain Y [auth A]	EA [auth B], FA [auth B], GA [auth B], Y [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain Y [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain Y [auth A]
W (Subject of Investigation/LOI) Query on W Download Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [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 C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Z [auth B]	K [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] J [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], J [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
H2S (Subject of Investigation/LOI) Query on H2S Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.213 (Depositor), 0.217 (DCC)
R-Value Work: 0.172 (Depositor), 0.182 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.396	α = 90
b = 123.099	β = 90
c = 147.189	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
pointless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BII-BBF/2050/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	2023.00286.BD
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0140/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0087/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04612/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04612/2020