9SQ3 | pdb_00009sq3

Crystal structure of the Molybdenum-containing nitrogenase from Methanocaldococcus infernus refined to 1.21 A resolution - crystalline form B.

PDB DOI: https://doi.org/10.2210/pdb9SQ3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanocaldococcus infernus ME
Mutation(s): No

Deposited: 2025-09-19 Released: 2026-07-29
Deposition Author(s): Maslac, N., Torer, M.R., Bolte, P., Wagner, T.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free:
0.146 (Depositor), 0.150 (DCC)
R-Value Work:
0.121 (Depositor), 0.129 (DCC)
R-Value Observed:
0.122 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular basis of N2-fixation in a hyperthermophilic archaeon

Maslac, N., Torer, M.R., Bolte, P., Wagner, T.

To be published.

Macromolecule Content

Total Structure Weight: 221.49 kDa
Atom Count: 17,734
Modeled Residue Count: 1,868
Deposited Residue Count: 1,878
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	A, C	477	Methanocaldococcus infernus ME	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for D5VU98 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME)) Explore D5VU98 Go to UniProtKB: D5VU98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5VU98
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase	B, D	462	Methanocaldococcus infernus ME	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for D5VU97 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME)) Explore D5VU97 Go to UniProtKB: D5VU97
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5VU97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICS (Subject of Investigation/LOI) Query on ICS Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain M [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain M [auth A]	DA [auth C], M [auth A]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain M [auth A] Interactions & Density Focus chain DA [auth C] Focus chain M [auth A]
ICE Query on ICE Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain N [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain N [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain N [auth A]	EA [auth C], N [auth A]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₈ BJBPMDQXUSSDMI-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain N [auth A] Interactions & Density Focus chain EA [auth C] Focus chain N [auth A]
A1JPW (Subject of Investigation/LOI) Query on A1JPW Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain R [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain R [auth B]	JA [auth D], R [auth B]	FE(8)-S(7) CLUSTER, P1+ state conformer A Fe₈ S₇ DZYOHONNTYKRPX-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain R [auth B] Interactions & Density Focus chain JA [auth D] Focus chain R [auth B]
A1JPX (Subject of Investigation/LOI) Query on A1JPX Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain O [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain O [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain O [auth A]	FA [auth C], O [auth A]	FE(8)-S(7) CLUSTER, P1+ state conformer B Fe₈ S₇ DZYOHONNTYKRPX-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain O [auth A] Interactions & Density Focus chain FA [auth C] Focus chain O [auth A]
HCA (Subject of Investigation/LOI) Query on HCA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain E [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain E [auth A]	E [auth A], Z [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain E [auth A] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain Z [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain IA [auth D] SDF format, chain HA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D]	HA [auth D], IA [auth D], Q [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain HA [auth D] Focus chain IA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain HA [auth D] Focus chain IA [auth D] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] G [auth A] H [auth A] I [auth A] BA [auth C], CA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] 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 KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] 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 KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain QA [auth D] SDF format, chain SA [auth D] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth D]	QA [auth D] RA [auth D] SA [auth D] W [auth B] X [auth B] QA [auth D], RA [auth D], SA [auth D], W [auth B], X [auth B], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
H2S (Subject of Investigation/LOI) Query on H2S Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth C]	AA [auth C], F [auth A]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain U [auth B] Focus chain V [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain TA [auth D] MOL2 format, chain TA [auth D] mmCIF format, chain TA [auth D]	TA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain TA [auth D] Interactions & Density Focus chain TA [auth D]
UNX (Subject of Investigation/LOI) Query on UNX Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain P [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain P [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain P [auth A]	GA [auth C], P [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain GA [auth C] Focus chain P [auth A] Interactions & Density Focus chain GA [auth C] Focus chain P [auth A]