SMTL ID : 5a8w.1 (1 other biounit)

METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER WOLFEII AT 1. 8 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

COM.1: 9 residues within 4Å: Chain A: Y.336, F.446, Y.447 Chain B: F.361, S.365, Y.367 Chain C: L.120, R.123 Ligands: F43.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.123, A:Y.447 COM.6: 9 residues within 4Å: Chain D: Y.336, F.446, Y.447 Chain E: F.361, S.365, Y.367 Chain F: L.120, R.123 Ligands: F43.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Y.447, F:R.123

2 x TP7: Coenzyme B

TP7.2: 19 residues within 4Å: Chain A: R.274, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain B: F.362, Y.367, G.368, G.369, H.379, V.380, V.381 Chain D: R.229, K.260, H.261 19 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:F.362, B:Y.367, B:Y.367, B:V.380, B:V.381, A:M.327, A:F.333 Hydrogen bonds: B:Y.367, B:G.369, D:K.260 Water bridges: B:G.369, A:R.274, D:R.229, D:R.229 Salt bridges: B:H.379, A:R.274, D:R.229, D:K.260, D:K.260 TP7.4: 19 residues within 4Å: Chain A: R.229, K.260, H.261 Chain D: R.274, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain E: F.362, Y.367, G.368, G.369, H.379, V.380, V.381 19 PLIP interactions: 8 interactions with chain E, 4 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: E:F.362, E:Y.367, E:Y.367, E:V.380, E:V.381, D:M.327, D:F.333 Hydrogen bonds: E:G.369, A:K.260, A:K.260 Water bridges: E:G.369, D:R.274, A:R.229, A:R.229 Salt bridges: E:H.379, D:R.274, A:R.229, A:K.260, A:K.260

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: E.163, D.164, D.520 Chain D: K.53, R.54 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Salt bridges: D:K.53, D:R.54 Hydrophobic interactions: A:D.520 Hydrogen bonds: A:D.520 ACT.8: 5 residues within 4Å: Chain A: K.53, R.54 Chain D: E.163, D.164, D.520 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Salt bridges: A:K.53, A:R.54 Hydrophobic interactions: D:D.520 ACT.9: 3 residues within 4Å: Chain E: K.43, M.121, G.122 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:M.121 Water bridges: E:K.43, E:K.43, B:K.43 Salt bridges: E:K.43, B:K.43 ACT.10: 6 residues within 4Å: Chain A: I.265, E.266, T.289, N.509 Chain E: N.67, R.163 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.265 Hydrogen bonds: A:E.266, A:N.509 Water bridges: E:R.163 Salt bridges: E:R.163 ACT.11: 5 residues within 4Å: Chain F: N.17, H.21, Y.26, E.144, I.216 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:N.17 Hydrogen bonds: F:Y.26 Salt bridges: F:H.21

2 x F43: FACTOR 430(Non-covalent)

F43.5: 32 residues within 4Å: Chain A: A.148, V.149, V.150, Q.151, M.154, Q.234, M.237, A.247 Chain D: G.329, G.330, V.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, G.445, F.446 Chain E: S.365, I.366, Y.367 Chain F: L.120, S.121, G.122, A.156, T.157, V.158, H.159, H.161 Ligands: COM.6 37 PLIP interactions: 14 interactions with chain D, 13 interactions with chain F, 7 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: D:V.331, D:F.333, D:Y.336, D:Y.336, D:F.399, D:F.446, F:L.120, A:Q.151, A:A.247 Hydrogen bonds: D:V.331, D:G.332, D:Q.335, D:Q.335, D:Y.336, D:Y.336, F:S.121, F:G.122, F:R.123, F:T.157, F:V.158, A:V.149, A:V.150, A:Q.151, A:Q.234, E:I.366, E:Y.367, E:Y.367 Water bridges: D:T.334, D:S.402, F:S.121, F:H.159, F:G.160, F:G.160, F:H.161, A:A.247 Salt bridges: F:H.159, F:H.161 F43.7: 32 residues within 4Å: Chain A: G.329, G.330, V.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, G.445, F.446 Chain B: S.365, I.366, Y.367 Chain C: L.120, S.121, G.122, A.156, T.157, V.158, H.159, H.161 Chain D: A.148, V.149, V.150, Q.151, M.154, Q.234, M.237, A.247 Ligands: COM.1 35 PLIP interactions: 13 interactions with chain C, 12 interactions with chain A, 2 interactions with chain B, 8 interactions with chain D, Hydrophobic interactions: C:L.120, A:V.331, A:F.333, A:Y.336, A:Y.336, A:F.399, A:F.446, D:V.150, D:Q.151 Hydrogen bonds: C:S.121, C:G.122, C:T.157, C:V.158, A:V.331, A:G.332, A:Q.335, A:Q.335, A:Y.336, B:I.366, B:Y.367, D:V.149, D:V.150, D:Q.151, D:Q.234 Water bridges: C:S.121, C:S.121, C:H.159, C:G.160, C:G.160, C:H.161, A:T.334, D:Q.151, D:A.247 Salt bridges: C:H.159, C:H.161

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

NA.12: 4 residues within 4Å: Chain F: N.224, I.225, A.226, D.229 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.226, F:D.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-08-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

METHYL-COENZYME M II REDUCTASE

METHYL-COENZYME M REDUCTASE II

METHYL-COENZYME M REDUCTASE II

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