9HPX | pdb_00009hpx

[FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand.

PDB DOI: https://doi.org/10.2210/pdb9HPX/pdb

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

Deposited: 2024-12-16 Released: 2025-12-24
Deposition Author(s): Carr, S.B., Duan, Z., Rodriguez-Macia, P.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.96 Å
R-Value Free:
0.144 (Depositor), 0.150 (DCC)
R-Value Work:
0.127 (Depositor), 0.137 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

To Bridge or not to Bridge: Manipulation of the Diatomic Ligands in Semi-synthetic [FeFe]-Hydrogenases Allows Isolation of a Novel Active-site State

Duan, Z., Gellet, J., Zamander, A., Bjornsson, R., Lachmann, M.T., Martini, M.A., Lorenzi, M., Myers, W.K., Berggren, G., Carr, S.B., Rodriguez-Macia, P.

To be published.

Macromolecule Content

Total Structure Weight: 55.27 kDa
Atom Count: 4,426
Modeled Residue Count: 485
Deposited Residue Count: 485
Unique protein chains: 2

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	A	397	Desulfovibrio desulfuricans	Mutation(s): 0 Gene Names: hydA, DVU_1769 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07598
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [Fe] hydrogenase small subunit	B	88	Desulfovibrio desulfuricans	Mutation(s): 0 Gene Names: hydB, DVU_1770 EC: 1.12.7.2
UniProt
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 Group	P07603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IW2 (Subject of Investigation/LOI) Query on A1IW2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	6,6,7,7-tetrakis($l^{3}-oxidanylidynemethyl)-1$l^{3},5$l^{3}-dithia-3-aza-6$l^{5},7$l^{4}-diferrabicyclo[3.1.1]heptane-6-carbonitrile C₇ H₅ Fe₂ N₂ O₄ S₂ XFZOTBOGDANNAV-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [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] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [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]
LI Query on LI Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	Q [auth A], R [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]