9R5I | pdb_00009r5i

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3

PDB DOI: https://doi.org/10.2210/pdb9R5I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
Mutation(s): No

Deposited: 2025-05-08 Released: 2025-10-22
Deposition Author(s): Jespersen, M., Lemaire, O.N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free:
0.206 (Depositor), 0.194 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.

Jespersen, M., Lorent, C., Lemaire, O.N., Zebger, I., Wagner, T.

(2025) Chembiochem 26: e202500692-e202500692

PubMed: 41078086 Search on PubMed
DOI: https://doi.org/10.1002/cbic.202500692
Primary Citation Related Structures:
9R51, 9R52, 9R5I, 9R6Z

PubMed Abstract:
Hydrogenases catalyze reversible H ₂ production and are potential models for renewable energy catalysts. Here, the full redox landscape of a group 3 [NiFe]-hydrogenase from methanothermococcus thermolithotrophicus is elucidated, resembling group 1 enzymes. Structural and spectroscopic analyses reveal a catalytic-ready state with nickel seesaw coordination, enabling intermediate trapping and advancing mechanistic understanding of oxygen-sensitive [NiFe] enzymes.

Organizational Affiliation

Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.

Macromolecule Content

Total Structure Weight: 214.3 kDa
Atom Count: 14,481
Modeled Residue Count: 1,828
Deposited Residue Count: 1,866
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha	A, D	410	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60338 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60338 Go to UniProtKB: Q60338
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60338
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta	B, F	282	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60341 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60341 Go to UniProtKB: Q60341
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60341
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma	C, E	241	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60340 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60340 Go to UniProtKB: Q60340
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain Q [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain Q [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain Q [auth B]	AB [auth F], Q [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AB [auth F] Focus chain Q [auth B] Interactions & Density Focus chain AB [auth F] Focus chain Q [auth B]
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain Z [auth C]	Z [auth C]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain Z [auth C] Interactions & Density Focus chain Z [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E]	DA [auth C] EA [auth C] EB [auth F] FA [auth C] X [auth B] DA [auth C], EA [auth C], EB [auth F], FA [auth C], X [auth B], XA [auth E], YA [auth E], ZA [auth E]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
NFU (Subject of Investigation/LOI) Query on NFU Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A]	JA [auth D], K [auth A]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain K [auth A] Interactions & Density Focus chain JA [auth D] Focus chain K [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain TA [auth E] MOL2 format, chain TA [auth E] mmCIF format, chain TA [auth E]	TA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain TA [auth E] Interactions & Density Focus chain TA [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth F] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	AA [auth C] BB [auth F] CB [auth F] DB [auth F] LA [auth D] AA [auth C], BB [auth F], CB [auth F], DB [auth F], LA [auth D], M [auth A], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain LA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain LA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain Y [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain Y [auth C]	G [auth A] HA [auth D] I [auth A] IA [auth D] J [auth A] G [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], UA [auth E], VA [auth E], WA [auth E], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth C] Interactions & Density Focus chain G [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain GA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	BA [auth C] CA [auth C] GA [auth D] MA [auth D] N [auth A] BA [auth C], CA [auth C], GA [auth D], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], RA [auth D], SA [auth D], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A]	KA [auth D], L [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain KA [auth D] Focus chain L [auth A] Interactions & Density Focus chain KA [auth D] Focus chain L [auth A]