SMTL ID : 1mro.1

METHYL-COENZYME M REDUCTASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: R.101, S.214, R.215, C.217 Chain D: R.101, S.214, R.215, C.217 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:R.215, D:C.217, A:R.215, A:C.217

2 x F43: FACTOR 430(Non-covalent)

F43.2: 34 residues within 4Å: Chain A: A.143, V.144, V.145, Q.146, M.149, Q.229, M.232, I.235, A.242 Chain D: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.441, F.442 Chain E: S.364, I.365, Y.366 Chain F: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 Ligands: COM.10 38 PLIP interactions: 13 interactions with chain D, 15 interactions with chain F, 7 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.442, F:L.116, F:V.154, A:I.235 Hydrogen bonds: D:V.327, D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, F:S.117, F:G.118, F:R.119, F:S.153, F:V.154, F:G.156, A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366 Water bridges: D:T.330, D:S.398, F:S.117, F:H.155, F:H.157, F:H.157, F:H.157, A:Q.146, A:E.147 Salt bridges: F:H.155, F:H.157 F43.9: 34 residues within 4Å: Chain A: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.441, F.442 Chain B: S.364, I.365, Y.366 Chain C: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 Chain D: A.143, V.144, V.145, Q.146, M.149, Q.229, M.232, I.235, A.242 Ligands: COM.5 36 PLIP interactions: 14 interactions with chain C, 2 interactions with chain B, 7 interactions with chain D, 13 interactions with chain A, Hydrophobic interactions: C:L.116, D:Q.146, D:I.235, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442 Hydrogen bonds: C:S.117, C:G.118, C:R.119, C:S.153, C:V.154, C:G.156, B:I.365, B:Y.366, D:V.144, D:V.145, D:Q.146, D:Q.229, A:V.327, A:G.328, A:Q.331, A:Q.331, A:Y.332 Water bridges: C:S.117, C:H.155, C:H.155, C:H.157, C:H.157, D:Q.146, A:T.330, A:S.398 Salt bridges: C:H.155, C:H.157

2 x TP7: Coenzyme B(Non-functional Binders)(Non-covalent)

TP7.3: 20 residues within 4Å: Chain A: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain B: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.224, K.255, H.256 18 PLIP interactions: 8 interactions with chain B, 6 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: B:F.361, B:Y.366, B:I.379, B:V.380, A:L.319, A:F.329 Hydrogen bonds: B:Y.366, B:G.368, D:K.255 Water bridges: B:G.368, D:R.224, D:R.224, A:R.269 Salt bridges: B:H.378, D:R.224, D:K.255, D:K.255, A:R.269 TP7.4: 20 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 18 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: E:F.361, E:Y.366, E:I.379, E:V.380, D:M.323, D:F.329 Hydrogen bonds: E:Y.366, E:G.368, A:K.255 Water bridges: E:G.368, E:H.378, A:R.224, A:R.224 Salt bridges: E:H.378, D:R.269, A:R.224, A:K.255, A:K.255

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

COM.5: 9 residues within 4Å: Chain A: Y.332, F.442, Y.443 Chain B: F.360, S.364, Y.366 Chain C: L.116, R.119 Ligands: F43.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.443 Water bridges: C:R.119 Salt bridges: C:R.119 COM.10: 9 residues within 4Å: Chain D: Y.332, F.442, Y.443 Chain E: F.360, S.364, Y.366 Chain F: L.116, R.119 Ligands: F43.2 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:Y.443 Water bridges: F:R.119, F:R.119 Salt bridges: F:R.119

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.223, R.224, K.255, H.261, E.274 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.223, A:R.224 Water bridges: A:R.224, A:R.224, A:R.224, A:E.274, A:E.274, D:R.269 GOL.7: 4 residues within 4Å: Chain A: D.169, D.173, D.182, N.184 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.169, A:D.173, A:D.182, A:N.184 Water bridges: A:D.182, A:I.183, A:I.183 GOL.11: 5 residues within 4Å: Chain D: D.169, A.172, D.173, D.182, N.184 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.184, D:N.184 Water bridges: D:D.182, D:I.183 GOL.12: 5 residues within 4Å: Chain D: S.223, R.224, K.255, H.261, E.274 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.223, D:R.224, D:E.274 Water bridges: D:R.224, D:R.224, D:R.224, D:E.274

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain C: E.29 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.134, C:K.134 NA.13: 1 residues within 4Å: Chain F: E.29 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.29 Water bridges: F:E.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ermler, U. et al., Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science (1997)

Release Date

1998-11-11

Peptides

METHYL-COENZYME M REDUCTASE: AD
METHYL-COENZYME M REDUCTASE: BE
METHYL-COENZYME M REDUCTASE: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

METHYL-COENZYME M REDUCTASE

METHYL-COENZYME M REDUCTASE

METHYL-COENZYME M REDUCTASE

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