30JK | pdb_000030jk

crystal structure of [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii in Hinact state

PDB DOI: https://doi.org/10.2210/pdb30JK/pdb
Entry: 30JK supersedes: 6TTL

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

Deposited: 2026-04-29 Released: 2026-08-12
Deposition Author(s): Duan, J., Rutz, A., Hofmann, E., Happe, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.280 (Depositor), 0.278 (DCC)
R-Value Work:
0.249 (Depositor), 0.249 (DCC)
R-Value Observed:
0.251 (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

Direct Binding of Cysteine-367 Thiolate to the Active Site of the [FeFe]-Hydrogenase from Clostridium beijerinckii in the O2-Stable State

Duan, J., Arrigoni, F., Rutz, A., Hofmann, E., Greco, C., Happe, T.

(2026) Biochemistry

DOI: https://doi.org/10.1021/acs.biochem.6c00395

Macromolecule Content

Total Structure Weight: 155.8 kDa
Atom Count: 10,171
Modeled Residue Count: 1,192
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[FeFe]-hydrogenase	A, B	674	Clostridium beijerinckii	Mutation(s): 0
UniProt
Find proteins for A0A1I9RYV3 (Clostridium beijerinckii) Explore A0A1I9RYV3 Go to UniProtKB: A0A1I9RYV3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I9RYV3
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 Y [auth B] SDF format, chain C [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain C [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain C [auth A]	C [auth A], Y [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 Y [auth B] Interactions & Density Focus chain C [auth A] Focus chain Y [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] D [auth A] E [auth A] F [auth A] AA [auth B], BA [auth B], D [auth A], E [auth A], F [auth A], Z [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain Z [auth B]
UNK Query on UNK Download:Ideal Coordinates CCD File	JA [auth B] KA [auth B] LA [auth B] M [auth A] MA [auth B] JA [auth B], KA [auth B], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A]	UNKNOWN C₄ H₉ N O₂ QWCKQJZIFLGMSD-VKHMYHEASA-N		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain CA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth B]	CA [auth B], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain G [auth A] Interactions & Density Focus chain CA [auth B] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B] FA [auth B] GA [auth B] HA [auth B] I [auth A] EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth B]	DA [auth B], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain H [auth A] Interactions & Density Focus chain DA [auth B] Focus chain H [auth A]