SMTL ID : 9h1l.1

Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x F43: FACTOR 430(Covalent)

F43.1: 33 residues within 4Å: Chain B: L.120, S.121, G.122, R.123, A.157, T.158, V.159, H.160, H.162 Chain E: S.365, I.366, Y.367 Chain F: 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 27 PLIP interactions: 8 interactions with chain B, 13 interactions with chain F, 3 interactions with chain E, 3 interactions with chain G, Hydrogen bonds: B:S.121, B:G.122, B:T.158, B:V.159, B:V.159, F:I.331, F:G.332, F:Q.335, F:Q.335, F:Y.336, F:F.399, E:I.366, E:Y.367, G:V.149, G:V.150, G:Q.234 Salt bridges: B:R.123, B:H.160, B:H.162 Hydrophobic interactions: F:I.331, F:F.333, F:Q.335, F:Y.336, F:Y.336, F:F.399, F:F.446, E:Y.367 F43.2: 29 residues within 4Å: Chain C: Q.89, L.120, S.121, G.122, R.123, A.157, V.159, H.160, H.162 Chain D: I.366, Y.367 Chain F: Q.151, M.154, M.233, M.237, I.240, A.247 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.5 23 PLIP interactions: 14 interactions with chain G, 6 interactions with chain C, 2 interactions with chain D, 1 interactions with chain F, Hydrophobic interactions: G:I.331, G:I.331, G:Y.336, G:Y.336, G:F.399, G:F.399, G:F.399, G:F.446, C:V.159, D:Y.367 Hydrogen bonds: G:G.329, G:T.334, G:Q.335, G:Q.335, G:Y.336, G:Y.336, C:S.121, C:G.122, D:Y.367, F:Q.151 Salt bridges: C:R.123, C:H.160, C:H.162

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

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

1 x TP7: Coenzyme B

TP7.4: 19 residues within 4Å: Chain E: F.361, F.362, Y.367, G.368, G.369, H.379, V.381 Chain F: 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 15 PLIP interactions: 7 interactions with chain E, 4 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: E:F.361, E:F.362, E:Y.367, E:V.381, F:L.323, F:M.327 Hydrogen bonds: E:Y.367, E:G.369, F:M.327, G:K.260 Salt bridges: E:H.379, F:R.274, G:R.229, G:K.260, G:K.260

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

SHT.5: 15 residues within 4Å: Chain C: L.120, R.123 Chain D: F.361, Y.367 Chain G: R.275, W.322, L.323, M.327, F.333, Y.336, F.446, Y.447, A.482, M.483 Ligands: F43.2 11 PLIP interactions: 6 interactions with chain G, 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: G:L.323, G:M.327, G:F.446, D:F.361, D:F.361, D:Y.367, D:Y.367 Hydrogen bonds: G:Y.447, G:A.482, G:M.483 Salt bridges: C:R.123

3 x S5Q: FeFe cofactor(Non-covalent)

S5Q.6: 16 residues within 4Å: Chain H: Y.17, P.141, E.142, G.143 Chain I: P.78, H.84, A.112, G.113, K.114, M.137, G.138, N.139, F.140, C.143, K.147, R.178 2 PLIP interactions: 2 interactions with chain I, Metal complexes: I:H.84, I:C.143 S5Q.7: 15 residues within 4Å: Chain F: H.142, V.150, E.152 Chain J: M.79, R.84, H.85, G.112, G.114, F.148, G.149, N.150, V.151, H.154, K.158, R.213 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain F, Metal complexes: J:H.85, J:H.154 Salt bridges: F:E.152, F:E.152 S5Q.8: 14 residues within 4Å: Chain I: L.85, C.90, S.93, R.97, M.105 Chain J: 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 J, Metal complexes: J:C.48, J:C.91

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain K: C.69, C.72, C.85, C.87, E.88 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.69, K:C.72, K:C.85, K:C.87

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.10: 20 residues within 4Å: Chain K: Y.13, V.18, R.37, S.38, G.39, A.40, G.41, K.42, S.43, V.44, Q.117, K.424, S.427, E.428, L.429, S.430, V.431, E.433, T.458 Ligands: MG.13 19 PLIP interactions: 19 interactions with chain K Hydrogen bonds: K:G.39, K:G.39, K:A.40, K:G.41, K:K.42, K:S.43, K:V.44, K:Q.117, K:K.424, K:S.427, K:S.430, K:S.430, K:V.431, K:V.431, K:E.433, K:T.458 Salt bridges: K:K.42, K:K.42 pi-Stacking: K:Y.13 ATP.11: 19 residues within 4Å: Chain K: R.162, H.165, D.169, L.170, S.171, G.173, E.174, Y.290, V.298, A.300, S.320, G.321, A.322, G.323, K.324, T.325, T.326, Q.373 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:R.162, K:S.171, K:G.173, K:E.174, K:G.321, K:G.321, K:A.322, K:G.323, K:K.324, K:T.325, K:T.326, K:T.326 Salt bridges: K:K.324, K:K.324 pi-Stacking: K:Y.290, K:Y.290

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain K: T.325, Q.373 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.325 MG.13: 3 residues within 4Å: Chain K: S.43, Q.117 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.43

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

UPF0288 protein MmarC6_0796: A
Methyl-coenzyme M reductase subunit gamma: BC
Methyl-coenzyme M reductase subunit beta: DE
Methyl-coenzyme M reductase subunit alpha: FG
Methanogenesis marker protein 17: H
Methanogenesis marker protein 7: I
Methyl-coenzyme M reductase operon protein C: J
Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA: K
DUF2098 domain-containing protein: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
A

C
B

D
E

E
D

F
C

G
F

H
G

I
H

J
I

K
K

L
L

UPF0288 protein MmarC6_0796

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

Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA

DUF2098 domain-containing protein

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