SMTL ID : 1e6v.1

Methyl-coenzyme M reductase from Methanopyrus kandleri

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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.147, V.148, V.149, Q.150, M.153, Q.233, M.236, A.246 Chain D: G.329, G.330, V.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, Q.403, G.445, F.446 Chain E: S.366, I.367, Y.368 Chain F: S.122, G.123, R.124, A.157, T.158, V.159, H.160, G.161, H.162 Ligands: COM.3 28 PLIP interactions: 9 interactions with chain F, 7 interactions with chain A, 3 interactions with chain E, 9 interactions with chain D, Hydrophobic interactions: F:V.159, A:Q.150, A:A.246, D:V.331, D:F.333, D:Y.336, D:Y.336 Hydrogen bonds: F:S.122, F:G.123, F:R.124, F:T.158, F:V.159, F:H.160, A:V.148, A:V.149, A:Q.150, A:Q.150, A:Q.233, E:I.367, E:Y.368, E:Y.368, D:G.332, D:T.334, D:Q.335, D:Q.335, D:Y.336 Salt bridges: F:H.160, F:H.162 F43.4: 34 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, Q.403, G.445, F.446 Chain B: S.366, I.367, Y.368 Chain C: S.122, G.123, R.124, A.157, T.158, V.159, H.160, G.161, H.162 Chain D: A.147, V.148, V.149, Q.150, M.153, Q.233, M.236, A.246 Ligands: COM.6 28 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B, 7 interactions with chain D, 9 interactions with chain A, Hydrophobic interactions: C:V.159, D:Q.150, D:A.246, A:V.331, A:F.333, A:Y.336, A:Y.336 Hydrogen bonds: C:S.122, C:G.123, C:R.124, C:T.158, C:V.159, C:H.160, B:I.367, B:Y.368, B:Y.368, D:V.148, D:V.149, D:Q.150, D:Q.150, D:Q.233, A:G.332, A:T.334, A:Q.335, A:Q.335, A:Y.336 Salt bridges: C:H.160, C:H.162

2 x TP7: Coenzyme B(Non-covalent)

TP7.2: 19 residues within 4Å: Chain A: R.273, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain B: F.362, F.363, Y.368, G.369, G.370, H.380, V.382 Chain D: R.228, K.259, H.260 15 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:F.363, B:Y.368, B:Y.368, B:V.382, A:M.327, A:F.333 Hydrogen bonds: B:G.370, D:K.259, D:K.259 Salt bridges: B:H.380, A:R.273, D:R.228, D:K.259, D:K.259, D:H.260 TP7.5: 19 residues within 4Å: Chain A: R.228, K.259, H.260 Chain D: R.273, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain E: F.362, F.363, Y.368, G.369, G.370, H.380, V.382 15 PLIP interactions: 3 interactions with chain D, 6 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: D:M.327, D:F.333, E:F.363, E:Y.368, E:Y.368, E:V.382 Salt bridges: D:R.273, E:H.380, A:R.228, A:K.259, A:K.259, A:H.260 Hydrogen bonds: E:G.370, A:K.259, A:K.259

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

COM.3: 9 residues within 4Å: Chain D: Y.336, F.446, Y.447 Chain E: F.362, S.366, Y.368 Chain F: L.121, R.124 Ligands: F43.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Y.447 Salt bridges: F:R.124 COM.6: 9 residues within 4Å: Chain A: Y.336, F.446, Y.447 Chain B: F.362, S.366, Y.368 Chain C: L.121, R.124 Ligands: F43.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.124 Hydrogen bonds: A:Y.447

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

METHYL-COENZYME M REDUCTASE I BETA SUBUNIT

METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT