SMTL ID : 5a0y.1

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

hetero-2-2-2-mer

Ligands

16 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: K.11, F.14, E.15 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.11, A:F.14, H2O.2, H2O.2, H2O.2, H2O.2 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: D.271 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.271, H2O.43, H2O.43, H2O.43, H2O.43, H2O.48 MG.13: 2 residues within 4Å: Chain C: E.30, K.135 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.30, H2O.51, H2O.51, H2O.51, H2O.55 MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain D: K.11, F.14, E.15 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:K.11, D:F.14, H2O.61, H2O.61, H2O.61, H2O.61 MG.22: 1 residues within 4Å: Chain D: E.175 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.175, H2O.71 MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain E: D.147 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.147, H2O.90, H2O.90, H2O.90, H2O.98 MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain F: E.30, K.135 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.30, H2O.100, H2O.100, H2O.101, H2O.104 MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x F43: FACTOR 430(Non-covalent)

F43.3: 35 residues within 4Å: Chain A: A.144, V.145, V.146, Q.147, M.150, M.229, Q.230, M.233, I.236, A.243 Chain D: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain E: S.365, I.366, Y.367 Chain F: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Ligands: COM.17 38 PLIP interactions: 12 interactions with chain D, 8 interactions with chain A, 3 interactions with chain E, 15 interactions with chain F, Hydrophobic interactions: D:V.328, D:F.330, D:Y.333, D:Y.333, D:F.396, D:F.443, A:Q.147, A:I.236, A:A.243, F:L.117 Hydrogen bonds: D:G.329, D:Q.332, D:Q.332, D:Y.333, D:Y.333, A:V.145, A:V.146, A:Q.147, A:Q.230, E:I.366, E:Y.367, E:Y.367, F:S.118, F:G.119, F:R.120, F:S.154, F:V.155 Water bridges: D:T.331, A:A.243, F:S.118, F:S.118, F:G.152, F:H.156, F:G.157, F:G.157, F:H.158 Salt bridges: F:H.156, F:H.158 F43.16: 35 residues within 4Å: Chain A: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain B: S.365, I.366, Y.367 Chain C: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Chain D: A.144, V.145, V.146, Q.147, M.150, M.229, Q.230, M.233, I.236, A.243 Ligands: COM.4 34 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B, 11 interactions with chain A, 14 interactions with chain C, Hydrophobic interactions: D:Q.147, D:I.236, A:V.328, A:F.330, A:Y.333, A:Y.333, A:F.443, C:L.117 Hydrogen bonds: D:V.145, D:V.146, D:Q.147, D:Q.230, B:I.366, B:Y.367, A:G.329, A:Q.332, A:Q.332, A:Y.333, C:S.118, C:G.119, C:R.120, C:S.154, C:V.155 Water bridges: D:Q.147, A:T.331, A:S.399, C:S.118, C:H.156, C:H.156, C:G.157, C:G.157, C:H.158 Salt bridges: C:H.156, C:H.158

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

COM.4: 9 residues within 4Å: Chain A: Y.333, F.443, Y.444 Chain B: F.361, S.365, Y.367 Chain C: L.117, R.120 Ligands: F43.16 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.444 Water bridges: C:R.120, C:R.120 Salt bridges: C:R.120 COM.17: 9 residues within 4Å: Chain D: Y.333, F.443, Y.444 Chain E: F.361, S.365, Y.367 Chain F: L.117, R.120 Ligands: F43.3 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.120, F:R.120 Salt bridges: F:R.120 Hydrogen bonds: D:Y.444

2 x TP7: Coenzyme B

TP7.5: 20 residues within 4Å: Chain A: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain B: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Chain D: R.225, K.256, H.257 22 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: A:M.324, A:F.330, B:F.362, B:F.362, B:Y.367, B:Y.367, B:I.380, B:V.381 Water bridges: A:R.270, A:M.324, B:Y.367, B:G.369, D:R.225, D:R.225 Salt bridges: A:R.270, B:H.379, D:R.225, D:K.256, D:K.256 Hydrogen bonds: B:G.369, D:K.256, D:K.256 TP7.18: 20 residues within 4Å: Chain A: R.225, K.256, H.257 Chain D: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain E: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 20 PLIP interactions: 5 interactions with chain D, 8 interactions with chain E, 7 interactions with chain A Hydrophobic interactions: D:M.324, D:F.330, E:F.362, E:F.362, E:Y.367, E:Y.367, E:I.380, E:V.381 Water bridges: D:R.270, D:R.270, A:R.225, A:R.225 Salt bridges: D:R.270, E:H.379, A:R.225, A:K.256, A:K.256 Hydrogen bonds: E:G.369, A:K.256, A:K.256

1 x K: POTASSIUM ION(Non-covalent)

K.6: 8 residues within 4Å: Chain A: R.102, S.215, R.216, C.218 Chain D: R.102, S.215, R.216, C.218 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:R.216, A:C.218, D:R.216, D:C.218

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

NA.9: 4 residues within 4Å: Chain A: P.58, I.60, G.61, T.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.58 Water bridges: A:L.64 NA.20: 4 residues within 4Å: Chain D: P.58, I.60, G.61, T.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.62 Water bridges: D:L.64

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: S.237, K.240 Chain F: K.153 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: N.296, Y.297, E.298, D.299 Ligand excluded by PLIP

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

2016-05-11

Peptides

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

METHYL-COENZYME M REDUCTASE I SUBUNIT BETA

METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA

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