9R6Z | pdb_00009r6z

Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus

PDB DOI: https://doi.org/10.2210/pdb9R6Z/pdb

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

Deposited: 2025-05-13 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: 2.85 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (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 of 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: 424.86 kDa
Atom Count: 28,822
Modeled Residue Count: 3,656
Deposited Residue Count: 3,732
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase subunit alpha	A, D, G, J	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60338
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase subunit beta	B, E, H, K	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60341
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase subunit gamma	C, F, I, L	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 XA [auth H] SDF format, chain P [auth B] SDF format, chain NB [auth K] SDF format, chain JA [auth E] MOL2 format, chain XA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain NB [auth K] MOL2 format, chain JA [auth E] mmCIF format, chain XA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain NB [auth K] mmCIF format, chain JA [auth E]	JA [auth E], NB [auth K], P [auth B], XA [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain JA [auth E] Focus chain NB [auth K] Focus chain P [auth B] Focus chain XA [auth H] Interactions & Density Focus chain JA [auth E] Focus chain NB [auth K] Focus chain P [auth B] Focus chain XA [auth H]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain SB [auth L] SDF format, chain RB [auth L] SDF format, chain QB [auth L] SDF format, chain QA [auth F] SDF format, chain PB [auth K] SDF format, chain PA [auth F] SDF format, chain OA [auth F] SDF format, chain NA [auth E] SDF format, chain CB [auth I] SDF format, chain BB [auth I] SDF format, chain AB [auth I] MOL2 format, chain ZA [auth H] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth L] MOL2 format, chain RB [auth L] MOL2 format, chain QB [auth L] MOL2 format, chain QA [auth F] MOL2 format, chain PB [auth K] MOL2 format, chain PA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain CB [auth I] MOL2 format, chain BB [auth I] MOL2 format, chain AB [auth I] mmCIF format, chain ZA [auth H] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth L] mmCIF format, chain RB [auth L] mmCIF format, chain QB [auth L] mmCIF format, chain QA [auth F] mmCIF format, chain PB [auth K] mmCIF format, chain PA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain CB [auth I] mmCIF format, chain BB [auth I] mmCIF format, chain AB [auth I]	AB [auth I] BB [auth I] CB [auth I] NA [auth E] OA [auth F] AB [auth I], BB [auth I], CB [auth I], NA [auth E], OA [auth F], PA [auth F], PB [auth K], QA [auth F], QB [auth L], RB [auth L], SB [auth L], T [auth B], V [auth C], W [auth C], X [auth C], ZA [auth H]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CB [auth I] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain QB [auth L] Focus chain RB [auth L] Focus chain SB [auth L] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CB [auth I] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain QB [auth L] Focus chain RB [auth L] Focus chain SB [auth L] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain ZA [auth H]
NFU (Subject of Investigation/LOI) Query on NFU Download Ideal Coordinates CCD File SDF format, chain WA [auth G] SDF format, chain O [auth A] SDF format, chain MB [auth J] SDF format, chain IA [auth D] MOL2 format, chain WA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain MB [auth J] MOL2 format, chain IA [auth D] mmCIF format, chain WA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain MB [auth J] mmCIF format, chain IA [auth D]	IA [auth D], MB [auth J], O [auth A], WA [auth G]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain MB [auth J] Focus chain O [auth A] Focus chain WA [auth G] Interactions & Density Focus chain IA [auth D] Focus chain MB [auth J] Focus chain O [auth A] Focus chain WA [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain YA [auth H] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain SA [auth G] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain OB [auth K] SDF format, chain N [auth A] SDF format, chain MA [auth E] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain HB [auth J] SDF format, chain GB [auth J] SDF format, chain FB [auth J] SDF format, chain EB [auth J] SDF format, chain DB [auth J] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain OB [auth K] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain GB [auth J] MOL2 format, chain FB [auth J] MOL2 format, chain EB [auth J] MOL2 format, chain DB [auth J] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain OB [auth K] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain GB [auth J] mmCIF format, chain FB [auth J] mmCIF format, chain EB [auth J] mmCIF format, chain DB [auth J] mmCIF format, chain AA [auth D]	AA [auth D] DB [auth J] EB [auth J] FB [auth J] GB [auth J] AA [auth D], DB [auth J], EB [auth J], FB [auth J], GB [auth J], HB [auth J], KA [auth E], LA [auth E], M [auth A], MA [auth E], N [auth A], OB [auth K], Q [auth B], R [auth B], RA [auth G], SA [auth G], U [auth C], Y [auth D], YA [auth H], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain DB [auth J] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain OB [auth K] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain U [auth C] Focus chain Y [auth D] Focus chain YA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain DB [auth J] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain OB [auth K] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain U [auth C] Focus chain Y [auth D] Focus chain YA [auth H] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain VA [auth G] SDF format, chain UA [auth G] SDF format, chain TA [auth G] SDF format, chain S [auth B] SDF format, chain LB [auth J] SDF format, chain KB [auth J] SDF format, chain JB [auth J] SDF format, chain IB [auth J] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth D] MOL2 format, chain VA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain LB [auth J] MOL2 format, chain KB [auth J] MOL2 format, chain JB [auth J] MOL2 format, chain IB [auth J] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain VA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain LB [auth J] mmCIF format, chain KB [auth J] mmCIF format, chain JB [auth J] mmCIF format, chain IB [auth J] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IB [auth J], JB [auth J], KB [auth J], LB [auth J], S [auth B], TA [auth G], UA [auth G], VA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain S [auth B] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain S [auth B] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G]