SMTL ID : 8s7x.1

Methyl-coenzyme M reductase activation complex without the A2 component

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-1-1-1-1-1-mer

Ligands

2 x F43: FACTOR 430(Covalent)(Non-covalent)

F43.1: 32 residues within 4Å: Chain A: L.120, S.121, G.122, R.123, A.157, T.158, V.159, H.160, H.162 Chain D: I.366, Y.367 Chain E: G.329, G.330, I.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, Q.403, F.446 Chain G: A.148, V.149, V.150, Q.151, M.154, Q.234, M.237, A.247 Ligands: COM.3 29 PLIP interactions: 14 interactions with chain E, 8 interactions with chain A, 3 interactions with chain D, 4 interactions with chain G, Hydrophobic interactions: E:I.331, E:F.333, E:Q.335, E:Q.335, E:Y.336, E:F.399, E:F.446 Hydrogen bonds: E:I.331, E:G.332, E:Q.335, E:Q.335, E:Y.336, E:Y.336, E:F.399, A:S.121, A:G.122, A:T.158, A:V.159, A:V.159, D:I.366, D:Y.367, D:Y.367, G:V.149, G:V.150, G:Q.151, G:Q.234 Salt bridges: A:R.123, A:H.160, A:H.162 F43.4: 28 residues within 4Å: Chain B: L.120, S.121, G.122, R.123, A.157, H.160, H.162 Chain C: I.366, Y.367 Chain E: A.148, V.149, Q.151, M.154, M.233, M.237, I.240 Chain G: G.329, I.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, G.445, F.446 Ligands: SHT.2 19 PLIP interactions: 10 interactions with chain G, 2 interactions with chain E, 5 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: G:I.331, G:I.331, G:Y.336, G:Y.336, G:F.399, G:F.446, C:Y.367 Hydrogen bonds: G:G.329, G:T.334, G:Q.335, G:Y.336, E:V.149, E:Q.151, B:S.121, B:G.122, C:Y.367 Salt bridges: B:R.123, B:H.160, B:H.162

1 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)

SHT.2: 14 residues within 4Å: Chain B: L.120, R.123 Chain C: F.361, Y.367, V.381 Chain G: M.327, S.328, F.333, Y.336, F.446, Y.447, A.482, M.483 Ligands: F43.4 9 PLIP interactions: 5 interactions with chain G, 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: G:F.333, G:F.446, C:F.361, C:Y.367, C:Y.367 Hydrogen bonds: G:S.328, G:Y.447, G:N.484 Salt bridges: B:R.123

1 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.3: 9 residues within 4Å: Chain A: L.120, R.123 Chain D: F.361, S.365, Y.367 Chain E: Y.336, F.446, Y.447 Ligands: F43.1 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Y.447 Salt bridges: A:R.123

1 x TP7: Coenzyme B

TP7.5: 19 residues within 4Å: Chain D: F.361, F.362, Y.367, G.368, G.369, V.380, V.381 Chain E: R.274, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain G: R.229, K.260, H.261 14 PLIP interactions: 4 interactions with chain G, 7 interactions with chain D, 3 interactions with chain E Hydrogen bonds: G:K.260, D:Y.367, D:G.369 Salt bridges: G:R.229, G:K.260, G:K.260, D:H.379, E:R.274 Hydrophobic interactions: D:F.362, D:Y.367, D:V.380, D:V.381, E:M.327, E:F.333

3 x S5Q: FeFe cofactor(Non-covalent)

S5Q.6: 15 residues within 4Å: Chain F: Y.17, P.141, E.142, G.143 Chain H: P.78, H.84, A.112, G.113, M.137, G.138, N.139, F.140, C.143, K.147, R.178 2 PLIP interactions: 2 interactions with chain H, Metal complexes: H:H.84, H:C.143 S5Q.7: 14 residues within 4Å: Chain H: L.85, C.90, S.93, R.97, M.105 Chain I: V.46, C.48, R.49, L.60, A.61, A.67, C.91, R.98, V.106 2 PLIP interactions: 2 interactions with chain I, Metal complexes: I:C.48, I:C.91 S5Q.8: 14 residues within 4Å: Chain E: E.152 Chain I: M.79, R.84, H.85, G.112, G.113, G.114, F.148, G.149, N.150, V.151, H.154, K.158, R.213 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain I, Salt bridges: E:E.152, E:E.152 Metal complexes: I:H.85, I:H.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez-Amador, F. et al., Structure of the ATP-driven methyl-coenzyme M reductase activation complex. Nature (2025)

Release Date

2025-02-26

Peptides

Methyl-coenzyme M reductase subunit gamma: AB
Methyl-coenzyme M reductase subunit beta: CD
Methyl-coenzyme M reductase subunit alpha: EG
Methanogenesis marker protein 17: F
Methanogenesis marker protein 7: H
Methyl-coenzyme M reductase operon protein C: I
UPF0288 protein MmarC6_0796: J
DUF2098 domain-containing protein: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
D

E
C

G
F

F
G

H
H

I
I

J
J

K
L

Methyl-coenzyme M reductase subunit gamma

Methyl-coenzyme M reductase subunit beta

Methyl-coenzyme M reductase subunit alpha

Methanogenesis marker protein 17

Methanogenesis marker protein 7

Methyl-coenzyme M reductase operon protein C

UPF0288 protein MmarC6_0796

DUF2098 domain-containing protein

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