SMTL ID : 1e6y.1

Methyl-coenzyme M reductase from Methanosarcina barkeri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x F43: FACTOR 430(Non-covalent)

F43.1: 34 residues within 4Å: Chain A: A.157, V.158, V.159, Q.160, M.163, Q.243, M.246, A.256, G.257 Chain D: G.338, G.339, V.340, G.341, F.342, T.343, Q.344, Y.345, F.415, G.416, G.461, F.462 Chain E: S.362, I.363, Y.364 Chain F: L.117, S.118, G.119, R.120, A.153, T.154, V.155, H.156, H.158 Ligands: COM.8 35 PLIP interactions: 6 interactions with chain A, 3 interactions with chain E, 12 interactions with chain D, 14 interactions with chain F, Hydrogen bonds: A:V.158, A:V.159, A:Q.160, A:Q.243, E:I.363, E:Y.364, E:Y.364, D:V.340, D:G.341, D:Q.344, D:Q.344, D:Y.345, F:S.118, F:G.119, F:R.120, F:T.154, F:V.155 Water bridges: A:Q.160, A:A.256, D:T.343, D:Y.345, F:S.118, F:H.156, F:H.156, F:H.158, F:H.158, F:H.158 Hydrophobic interactions: D:V.340, D:F.342, D:Y.345, D:Y.345, D:F.462, F:L.117 Salt bridges: F:H.156, F:H.158 F43.6: 34 residues within 4Å: Chain A: G.338, G.339, V.340, G.341, F.342, T.343, Q.344, Y.345, F.415, G.416, G.461, F.462 Chain B: S.362, I.363, Y.364 Chain C: L.117, S.118, G.119, R.120, A.153, T.154, V.155, H.156, H.158 Chain D: A.157, V.158, V.159, Q.160, M.163, Q.243, M.246, A.256, G.257 Ligands: COM.3 36 PLIP interactions: 13 interactions with chain A, 14 interactions with chain C, 6 interactions with chain D, 3 interactions with chain B, Hydrophobic interactions: A:V.340, A:F.342, A:Y.345, A:Y.345, A:F.462, C:L.117 Hydrogen bonds: A:V.340, A:G.341, A:T.343, A:Q.344, A:Q.344, A:Y.345, C:S.118, C:G.119, C:R.120, C:T.154, C:V.155, D:V.158, D:V.159, D:Q.160, D:Q.243, B:I.363, B:Y.364, B:Y.364 Water bridges: A:T.343, A:S.418, C:S.118, C:H.156, C:H.156, C:H.158, C:H.158, C:H.158, D:Q.160, D:A.256 Salt bridges: C:H.156, C:H.158

2 x TP7: Coenzyme B(Non-covalent)

TP7.2: 20 residues within 4Å: Chain A: R.283, L.332, M.336, S.337, F.342, F.462, M.499, N.500, V.501 Chain B: F.358, F.359, Y.364, G.365, G.366, H.376, V.377, V.378 Chain D: R.238, K.269, H.270 20 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:F.359, B:Y.364, B:V.377, B:V.378, A:M.336, A:F.342 Hydrogen bonds: B:Y.364, B:G.366, D:K.269 Water bridges: B:Y.364, B:G.366, A:R.283, A:M.336, D:R.238, D:R.238 Salt bridges: B:H.376, A:R.283, D:R.238, D:K.269, D:K.269 TP7.7: 20 residues within 4Å: Chain A: R.238, K.269, H.270 Chain D: R.283, L.332, M.336, S.337, F.342, F.462, M.499, N.500, V.501 Chain E: F.358, F.359, Y.364, G.365, G.366, H.376, V.377, V.378 20 PLIP interactions: 5 interactions with chain D, 7 interactions with chain A, 8 interactions with chain E Hydrophobic interactions: D:M.336, D:F.342, E:F.359, E:Y.364, E:V.377, E:V.378 Water bridges: D:R.283, D:M.336, A:R.238, A:R.238, A:K.269, E:G.366 Salt bridges: D:R.283, A:R.238, A:K.269, A:K.269, E:H.376 Hydrogen bonds: A:K.269, E:Y.364, E:G.366

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

COM.3: 9 residues within 4Å: Chain A: Y.345, F.462, F.463 Chain B: F.358, S.362, Y.364 Chain C: L.117, R.120 Ligands: F43.6 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:F.463 Water bridges: C:R.120, C:R.120 Salt bridges: C:R.120 COM.8: 9 residues within 4Å: Chain D: Y.345, F.462, F.463 Chain E: F.358, S.362, Y.364 Chain F: L.117, R.120 Ligands: F43.1 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:F.463 Water bridges: F:R.120, F:R.120 Salt bridges: F:R.120

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.378, K.381, T.436, G.437, R.518 Chain E: G.67, R.68 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:R.518, E:G.67 Water bridges: A:K.378, A:K.381, E:R.68, E:R.68 GOL.5: 8 residues within 4Å: Chain A: K.269, H.270, L.273, V.274, S.275, E.278 Chain E: K.61, M.167 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.269, A:S.275, A:S.275 Water bridges: A:S.275, E:K.61 GOL.9: 7 residues within 4Å: Chain B: G.67, R.68 Chain D: K.378, K.381, T.436, G.437, R.518 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.67, B:R.68, D:R.518 Water bridges: B:R.68, D:R.518

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grabarse, W. et al., Comparison of Three Methyl-Coenzyme M Reductases from Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation. J.Mol.Biol. (2000)

Release Date

2000-10-18

Peptides

METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA: AD
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT: BE
METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA: 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 SUBUNIT ALPHA

METHYL-COENZYME M REDUCTASE I BETA SUBUNIT

METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA