SMTL ID : 5a8r.1 (1 other biounit)

METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARBURGENSIS AT 2.15 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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.361, S.365, Y.367 Chain C: L.120, R.123 Ligands: F43.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.123, C:R.123 Salt bridges: C:R.123 Hydrogen bonds: A:Y.446 COM.5: 9 residues within 4Å: Chain D: Y.335, F.445, Y.446 Chain E: F.361, S.365, Y.367 Chain F: L.120, R.123 Ligands: F43.3 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.123, F:R.123 Salt bridges: F:R.123 Hydrogen bonds: D:Y.446

2 x TP7: Coenzyme B

TP7.2: 18 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, M.482, N.483, V.484 Chain E: F.362, Y.367, G.368, G.369, H.379, V.380 15 PLIP interactions: 7 interactions with chain E, 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: E:F.362, E:Y.367, E:V.380, D:M.326 Hydrogen bonds: E:Y.367, E:G.369, A:K.259 Water bridges: E:G.369, A:R.228, D:R.273 Salt bridges: E:H.379, A:R.228, A:K.259, A:K.259, D:R.273 TP7.6: 19 residues within 4Å: Chain A: R.273, L.322, M.326, S.327, F.332, F.445, M.482, N.483, V.484 Chain B: F.362, Y.367, G.368, G.369, H.379, V.380, V.381 Chain D: R.228, K.259, H.260 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:V.380, B:V.381, A:M.326 Hydrogen bonds: B:Y.367, B:G.369, D:K.259 Water bridges: B:Y.367, B:G.369, A:R.273, A:M.326, D:R.228, D:R.228 Salt bridges: B:H.379, A:R.273, D:R.228, D:K.259, D:K.259

2 x F43: FACTOR 430(Non-covalent)

F43.3: 32 residues within 4Å: Chain A: A.147, V.148, V.149, Q.150, M.153, 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, G.444, F.445 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.5 37 PLIP interactions: 6 interactions with chain A, 15 interactions with chain F, 13 interactions with chain D, 3 interactions with chain E, Hydrogen bonds: A:V.148, A:V.149, A:Q.150, A:Q.233, F:S.121, F:G.122, F:R.123, F:T.157, F:V.158, F:G.160, D:V.330, D:G.331, D:Q.334, D:Q.334, D:Y.335, D:Y.335, E:I.366, E:Y.367, E:Y.367 Water bridges: A:Q.150, A:A.246, F:S.121, F:S.121, F:H.159, F:H.161, F:H.161, F:H.161, D:T.333 Hydrophobic interactions: F:L.120, D:V.330, D:F.332, D:Y.335, D:Y.335, D:F.398, D:F.445 Salt bridges: F:H.159, F:H.161 F43.7: 32 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, G.444, F.445 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.147, V.148, V.149, Q.150, M.153, Q.233, M.236, A.246 Ligands: COM.1 35 PLIP interactions: 7 interactions with chain D, 14 interactions with chain C, 12 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: D:Q.150, A:V.330, A:F.332, A:Y.335, A:Y.335, A:F.398, A:F.445 Hydrogen bonds: D:V.148, D:V.149, D:Q.150, D:Q.233, C:S.121, C:G.122, C:R.123, C:T.157, C:V.158, C:G.160, A:V.330, A:G.331, A:Q.334, A:Q.334, A:Y.335, B:I.366, B:Y.367 Water bridges: D:Q.150, D:A.246, C:S.121, C:S.121, C:H.159, C:H.159, C:H.161, C:H.161, A:T.333 Salt bridges: C:H.159, C:H.161

3 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: P.61, I.63, V.65 Chain D: H.141, A.147 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:I.63, A:V.65, D:A.147, H2O.23 K.8: 5 residues within 4Å: Chain A: H.141, A.147 Chain D: P.61, I.63, V.65 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:A.147, D:I.63, D:V.65, H2O.3 K.9: 6 residues within 4Å: Chain A: V.218, R.219, C.221 Chain D: V.218, R.219, C.221 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:V.218, D:R.219, D:C.221, A:R.219, A:C.221

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

2016-08-10

Peptides

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

METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA

METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA

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