9GNK | pdb_00009gnk

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum

PDB DOI: https://doi.org/10.2210/pdb9GNK/pdb
Entry: 9GNK supersedes: 8RU7

Classification: OXIDOREDUCTASE
Organism(s): Desulfovibrio desulfuricans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-03 Released: 2025-09-24
Deposition Author(s): Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.168 (Depositor), 0.169 (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

Enhancing maturation of [FeFe]-hydrogenase by interlinking the large and small subunits

Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.

To be published.

Macromolecule Content

Total Structure Weight: 56.89 kDa
Atom Count: 4,471
Modeled Residue Count: 485
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	A	492	Desulfovibrio desulfuricans	Mutation(s): 0 Gene Names: hydA, DVU_1769, hydB, DVU_1770 EC: 1.12.7.2
UniProt
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07598 Go to UniProtKB: P07598
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07603 Go to UniProtKB: P07603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P07603P07598
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
402 (Subject of Investigation/LOI) Query on 402 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) C₇ H₅ Fe₂ N₃ O₃ S₂ LJPDYWPSPOWMIB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	H [auth A], L [auth A], M [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CMO (Subject of Investigation/LOI) Query on CMO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]