MolNFT v1 · #5069 · protein

Methyl-coenzyme M reductase from methanopyrus kandleri

1E6V · Methyl-coenzyme M reductase I alpha subunit: “Methyl-coenzyme M reductase from methanopyrus kandleri”. X-ray diffraction, 3 ligands (F43, TP7, COM), 18 pockets (best druggability 0.89). MolNFT v1 #5069 on GenesisL1: 3D structure…

PDB: 1E6V
Type: protein
Length: 2,458 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-coenzyme M reductase I alpha subunit; Methyl-coenzyme M reductase I beta subunit…
UniProt: Q49605, Q49601, Q49604
Ligands: F43, TP7, COM
Pockets: 18 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Methyl-coenzyme M reductase I alpha subunit	protein	545	56% helix, 6% strand	Q49605
B, E	Methyl-coenzyme M reductase I beta subunit	protein	436	53% helix, 9% strand	Q49601
C, F	Methyl-coenzyme M reductase I gamma subunit	protein	248	30% helix, 17% strand	Q49604

Ligands and binding sites

F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains D, E, F, A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.89	0.95	73	F43, COM, TP7
2	1160	0.88	0.90	121	TP7, F43, COM
3	1103	0.78	0.80	74	empty
4	51	0.64	0.94	19	empty
5	346	0.55	0.75	47	empty

Interfaces

14 interfaces between chains.

A–D · 4941 Å² buried · 82 hydrogen bonds · protein-protein
B–C · 2638 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2635 Å² buried · 35 hydrogen bonds · protein-protein
D–F · 2465 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 2463 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

1E6V · Methyl-coenzyme M reductase from Methanopyrus kandleri · the same entry in another collection · chain F against F, TM-score 1.00
Q49605 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase I subunit alpha (Q49605) · a predicted model of the same protein · chain D against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q49605
Every structure of UniProt Q49601
Every structure of UniProt Q49604
Elsewhere: RCSB PDB 1E6V · PDBe 1E6V · UniProt Q49605 · UniProt Q49601 · UniProt Q49604

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.