SMTL ID : 5n2a.1

METHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS TRIGONAL FORM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.335, F.445, Y.446 Chain B: F.362, S.366, Y.368 Chain C: L.120, R.123 Ligands: F43.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.446 Salt bridges: C:R.123 COM.6: 9 residues within 4Å: Chain D: Y.335, F.445, Y.446 Chain E: F.362, S.366, Y.368 Chain F: L.120, R.123 Ligands: F43.8 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Salt bridges: F:R.123 Hydrogen bonds: D:Y.446

2 x TP7: Coenzyme B

TP7.2: 20 residues within 4Å: Chain A: R.273, L.322, M.326, S.327, F.332, F.445, A.481, M.482, N.483, V.484 Chain B: F.363, Y.368, G.369, G.370, H.380, I.381, V.382 Chain D: R.228, K.259, H.260 16 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: A:L.322, A:M.326, A:F.332, B:F.363, B:Y.368, B:Y.368, B:I.381, B:V.382 Hydrogen bonds: A:R.273, B:G.370, D:K.259, D:K.259 Salt bridges: B:H.380, D:R.228, D:K.259, D:K.259 TP7.7: 20 residues within 4Å: Chain A: R.228, K.259, H.260 Chain D: R.273, L.322, M.326, S.327, F.332, F.445, A.481, M.482, N.483, V.484 Chain E: F.363, Y.368, G.369, G.370, H.380, I.381, V.382 16 PLIP interactions: 4 interactions with chain D, 7 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: D:L.322, D:M.326, D:F.332, E:F.363, E:Y.368, E:Y.368, E:I.381, E:V.382 Hydrogen bonds: D:R.273, E:G.370, A:K.259, A:K.259 Salt bridges: E:H.380, A:R.228, A:K.259, A:K.259

2 x F43: FACTOR 430(Non-covalent)

F43.3: 34 residues within 4Å: Chain A: G.328, G.329, V.330, G.331, F.332, T.333, Q.334, Y.335, F.398, G.399, S.401, G.444, F.445 Chain B: S.366, I.367, Y.368 Chain C: L.120, S.121, G.122, A.157, T.158, V.159, H.160, H.162 Chain D: A.147, V.148, V.149, Q.150, M.153, M.232, Q.233, M.236, A.246 Ligands: COM.1 29 PLIP interactions: 12 interactions with chain A, 6 interactions with chain D, 8 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: A:V.330, A:F.332, A:Y.335, A:Y.335, A:F.445, D:V.149, D:Q.150, C:L.120 Hydrogen bonds: A:V.330, A:G.331, A:T.333, A:Q.334, A:Q.334, A:Y.335, A:Y.335, D:V.148, D:V.149, D:Q.150, D:Q.233, C:S.121, C:G.122, C:R.123, C:T.158, C:V.159, B:I.367, B:Y.368, B:Y.368 Salt bridges: C:H.160, C:H.162 F43.8: 34 residues within 4Å: Chain A: A.147, V.148, V.149, Q.150, M.153, M.232, Q.233, M.236, A.246 Chain D: G.328, G.329, V.330, G.331, F.332, T.333, Q.334, Y.335, F.398, G.399, S.401, G.444, F.445 Chain E: S.366, I.367, Y.368 Chain F: L.120, S.121, G.122, A.157, T.158, V.159, H.160, H.162 Ligands: COM.6 27 PLIP interactions: 8 interactions with chain F, 11 interactions with chain D, 2 interactions with chain E, 6 interactions with chain A, Hydrophobic interactions: F:L.120, D:V.330, D:F.332, D:Y.335, D:Y.335, D:F.445, A:V.149, A:Q.150 Hydrogen bonds: F:S.121, F:G.122, F:R.123, F:T.158, F:V.159, D:V.330, D:G.331, D:T.333, D:Q.334, D:Q.334, D:Y.335, E:I.367, E:Y.368, A:V.148, A:V.149, A:Q.150, A:Q.233 Salt bridges: F:H.160, F:H.162

2 x K: POTASSIUM ION(Non-covalent)

K.4: 9 residues within 4Å: Chain A: R.105, G.218, R.219, C.221 Chain D: R.105, G.218, R.219, C.221 Ligands: K.9 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.218, D:C.221, A:G.218, A:C.221 K.9: 9 residues within 4Å: Chain A: R.105, G.218, R.219, C.221 Chain D: R.105, G.218, R.219, C.221 Ligands: K.4 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.218, D:C.221, A:G.218, A:C.221

2 x BR: BROMIDE ION(Non-covalent)

BR.5: 3 residues within 4Å: Chain C: K.13, R.215, G.225 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain F: K.13, R.215, G.225 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales. J.Bacteriol. (2017)

Release Date

2017-06-14

Peptides

Methyl-coenzyme M reductase subunit alpha: AD
Methyl-coenzyme M reductase, beta subunit: BE
Methyl-coenzyme M reductase, gamma subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

Methyl-coenzyme M reductase subunit alpha

Methyl-coenzyme M reductase, beta subunit

Methyl-coenzyme M reductase, gamma subunit

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