9S8H | pdb_00009s8h

Nickel-bound [FeFe]-hydrogenase CpI from Clostridium pasteurianum

PDB DOI: https://doi.org/10.2210/pdb9S8H/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium pasteurianum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-05 Released: 2026-10-28
Deposition Author(s): Duan, J., Yang, Z., Hofmann, E., Happe, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (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

A Histidine-Mediated, Pendulum-Like Proton Transport Mechanism Is Required for the High Catalytic Activity of [FeFe]-Hydrogenases

Duan, J., Yang, Z., Lampret, O., Arrigoni, F., Impel, L.V., Zheng, F., Kleinhaus, J., Apfel, U.P., Greco, C., De Gioia, L., Hofmann, E., Hemschemeier, A., Happe, T.

(2026) J Am Chem Soc

DOI: https://doi.org/10.1021/jacs.6c14410

Macromolecule Content

Total Structure Weight: 134.86 kDa
Atom Count: 10,100
Modeled Residue Count: 1,152
Deposited Residue Count: 1,168
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron hydrogenase 1	A, B	584	Clostridium pasteurianum	Mutation(s): 0 EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum) Explore P29166 Go to UniProtKB: P29166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 Q [auth B] SDF format, chain C [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain C [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain C [auth A]	C [auth A], Q [auth B]	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] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] R [auth B] D [auth A], E [auth A], F [auth A], G [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth B] mmCIF format, chain H [auth A]	H [auth A], V [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain V [auth B] Interactions & Density Focus chain H [auth A] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth B] mmCIF format, chain J [auth A]	J [auth A], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain X [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], Y [auth B], Z [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] M [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [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 M [auth A] Focus chain N [auth A] Focus chain O [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain P [auth A] SDF format, chain I [auth A] SDF format, chain EA [auth B] MOL2 format, chain W [auth B] MOL2 format, chain P [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain W [auth B] mmCIF format, chain P [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth B]	EA [auth B], I [auth A], P [auth A], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain I [auth A] Focus chain P [auth A] Focus chain W [auth B] Interactions & Density Focus chain EA [auth B] Focus chain I [auth A] Focus chain P [auth A] Focus chain W [auth B]