9OQC | pdb_00009oqc

Methyl-coenzyme M Reductase red1/red1-silent ensemble cryo-capillary

PDB DOI: https://doi.org/10.2210/pdb9OQC/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Methanothermobacter marburgensis
Mutation(s): No

Deposited: 2025-05-20 Released: 2026-11-04
Deposition Author(s): Ohmer, C.J., Ragsdale, S.W.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.156 (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

Structure of active methyl-CoM reductase, Earth's main methane producer

Ohmer, C.J., Ragsdale, S.W.

To be published.

Macromolecule Content

Total Structure Weight: 276.43 kDa
Atom Count: 40,652
Modeled Residue Count: 2,476
Deposited Residue Count: 2,476
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit alpha	A, D [auth a]	548	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558 Go to UniProtKB: P11558
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11558
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit beta	B, E [auth b]	442	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560 Go to UniProtKB: P11560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11560
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit gamma	C, F [auth c]	248	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562 Go to UniProtKB: P11562
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 (Subject of Investigation/LOI) Query on F43 Download:Ideal Coordinates CCD File SDF format, chain V [auth a] SDF format, chain T [auth a] SDF format, chain I [auth A] MOL2 format, chain V [auth a] MOL2 format, chain T [auth a] MOL2 format, chain I [auth A] mmCIF format, chain V [auth a] mmCIF format, chain T [auth a] mmCIF format, chain I [auth A]	I [auth A], T [auth a], V [auth a]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain I [auth A] Focus chain T [auth a] Focus chain V [auth a] Interactions & Density Focus chain I [auth A] Focus chain T [auth a] Focus chain V [auth a]
TP7 Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain U [auth a] SDF format, chain G [auth A] MOL2 format, chain U [auth a] MOL2 format, chain G [auth A] mmCIF format, chain U [auth a] mmCIF format, chain G [auth A]	G [auth A], U [auth a]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain G [auth A] Focus chain U [auth a] Interactions & Density Focus chain G [auth A] Focus chain U [auth a]
COM (Subject of Investigation/LOI) Query on COM Download:Ideal Coordinates CCD File SDF format, chain W [auth a] SDF format, chain H [auth A] MOL2 format, chain W [auth a] MOL2 format, chain H [auth A] mmCIF format, chain W [auth a] mmCIF format, chain H [auth A]	H [auth A], W [auth a]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain W [auth a] Interactions & Density Focus chain H [auth A] Focus chain W [auth a]
4TI Query on 4TI Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	TITANIUM ION Ti VEOOXLFYKHRLHJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth a] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain AA [auth b] MOL2 format, chain X [auth a] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth b] mmCIF format, chain X [auth a] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth b]	AA [auth b] K [auth A] L [auth A] M [auth A] N [auth A] AA [auth b], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth C], X [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth b] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain X [auth a] Interactions & Density Focus chain AA [auth b] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain X [auth a]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth a] SDF format, chain Y [auth a] SDF format, chain S [auth C] SDF format, chain P [auth A] MOL2 format, chain Z [auth a] MOL2 format, chain Y [auth a] MOL2 format, chain S [auth C] MOL2 format, chain P [auth A] mmCIF format, chain Z [auth a] mmCIF format, chain Y [auth a] mmCIF format, chain S [auth C] mmCIF format, chain P [auth A]	P [auth A], S [auth C], Y [auth a], Z [auth a]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain S [auth C] Focus chain Y [auth a] Focus chain Z [auth a] Interactions & Density Focus chain P [auth A] Focus chain S [auth C] Focus chain Y [auth a] Focus chain Z [auth a]

Modified Residues 6 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MHS Query on MHS	A, D [auth a]	HIS	Methylation	C₇ H₁₁ N₃ O₂
AGM Query on AGM	A, D [auth a]	ARG	Methylation	C₇ H₁₇ N₄ O₂
MGN Query on MGN	A, D [auth a]	GLN	Methylation	C₆ H₁₂ N₂ O₃
GL3 Query on GL3	A, D [auth a]	GLY	Sulfhydration	C₂ H₅ N O S
DYA Query on DYA	A, D [auth a]	ASP	Dehydrogenation	C₄ H₅ N O₄
SMC Query on SMC	A, D [auth a]	CYS	Methylation	C₄ H₉ N O₂ S