SMTL ID : 1hbu.1

METHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPLEX with COENZYME M

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x F43: FACTOR 430(Non-covalent)

F43.1: 35 residues within 4Å: Chain A: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.441, F.442 Chain B: S.364, I.365, Y.366 Chain C: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 Chain D: A.143, V.144, V.145, Q.146, M.149, M.228, Q.229, M.232, I.235, A.242 Ligands: COM.3 34 PLIP interactions: 14 interactions with chain C, 7 interactions with chain D, 11 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: C:L.116, D:Q.146, D:I.235, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.442 Hydrogen bonds: C:S.117, C:G.118, C:R.119, C:S.153, C:V.154, D:V.144, D:V.145, D:Q.146, D:Q.229, A:G.328, A:T.330, A:Q.331, A:Q.331, A:Y.332, B:I.365, B:Y.366 Water bridges: C:S.117, C:H.155, C:H.155, C:G.156, C:G.156, C:H.157, D:Q.146, A:S.398 Salt bridges: C:H.155, C:H.157 F43.26: 35 residues within 4Å: Chain A: A.143, V.144, V.145, Q.146, M.149, M.228, Q.229, M.232, I.235, A.242 Chain D: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.441, F.442 Chain E: S.364, I.365, Y.366 Chain F: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 Ligands: COM.28 38 PLIP interactions: 13 interactions with chain D, 9 interactions with chain A, 3 interactions with chain E, 13 interactions with chain F, Hydrophobic interactions: D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.442, A:Q.146, A:I.235, F:L.116, F:V.154 Hydrogen bonds: D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366, F:S.117, F:G.118, F:S.153, F:V.154, F:G.156 Water bridges: D:T.330, D:G.397, D:S.398, A:Q.146, A:E.147, A:A.242, F:H.155, F:H.157, F:H.157, F:H.157 Salt bridges: F:H.155, F:H.157

2 x TP7: Coenzyme B(Non-covalent)

TP7.2: 19 residues within 4Å: Chain A: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain B: F.360, F.361, Y.366, G.367, G.368, H.378, V.380 Chain D: R.224, K.255, H.256 22 PLIP interactions: 5 interactions with chain A, 11 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: A:M.323, A:F.329, B:F.360, B:F.361, B:F.361, B:Y.366, B:V.380 Water bridges: A:R.269, A:M.323, B:Y.366, B:G.368, B:G.368, D:R.224, D:R.224 Salt bridges: A:R.269, B:H.378, D:R.224, D:K.255, D:K.255 Hydrogen bonds: B:Y.366, B:G.368, D:K.255 TP7.27: 19 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, V.380 20 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A, 9 interactions with chain E Hydrophobic interactions: D:M.323, E:F.360, E:F.361, E:F.361, E:Y.366, E:Y.366, E:V.380 Water bridges: D:R.269, D:R.269, A:R.224, A:R.224, E:G.368 Salt bridges: D:R.269, A:R.224, A:K.255, A:K.255, E:H.378 Hydrogen bonds: A:K.255, A:K.255, E:G.368

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

COM.3: 9 residues within 4Å: Chain A: Y.332, F.442, Y.443 Chain B: F.360, S.364, Y.366 Chain C: L.116, R.119 Ligands: F43.1 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.443 Water bridges: C:R.119, C:R.119 Salt bridges: C:R.119 COM.28: 9 residues within 4Å: Chain D: Y.332, F.442, Y.443 Chain E: F.360, S.364, Y.366 Chain F: L.116, R.119 Ligands: F43.26 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.119, F:R.119 Salt bridges: F:R.119 Hydrogen bonds: D:Y.443

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: S.223, R.224, K.255, H.261, E.274 Ligands: NA.11 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.223, A:S.223, A:R.224, A:E.274 Water bridges: A:R.224, A:R.224, A:R.224, A:H.261, A:E.274 GOL.5: 6 residues within 4Å: Chain A: D.169, A.172, D.173, V.180, D.182, N.184 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.173, A:D.182, A:N.184 Water bridges: A:D.173, A:D.182, A:D.182, A:D.182 GOL.6: 5 residues within 4Å: Chain A: V.518, K.530, E.535, F.536, E.537 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.530, A:E.535, A:E.537 Water bridges: A:E.527, A:K.530, A:E.537, A:P.538 GOL.7: 7 residues within 4Å: Chain A: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.3, A:Y.379 Water bridges: A:K.3, A:E.351 GOL.18: 6 residues within 4Å: Chain B: K.2, E.24, S.27, R.30, E.233 Chain E: V.94 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:V.94, B:S.27, B:S.27, B:R.30, B:R.30 GOL.24: 6 residues within 4Å: Chain C: I.72, Y.108, R.109, D.128, K.131, I.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.109, C:D.128, C:D.128 GOL.29: 5 residues within 4Å: Chain D: D.169, A.172, D.173, D.182, N.184 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.173, D:D.182, D:N.184 Water bridges: D:D.182, D:D.182, D:I.183 GOL.30: 6 residues within 4Å: Chain D: S.223, R.224, K.255, H.261, E.274 Ligands: NA.35 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.223, D:S.223, D:R.224, D:K.255 Water bridges: D:R.224, D:R.224, D:R.224, D:E.274, A:R.269 GOL.31: 11 residues within 4Å: Chain D: Q.290, R.293, F.512, A.513, D.514, D.515, L.517, F.519, D.520, F.521, T.522 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.290, D:R.293, D:F.512, D:D.514, D:D.515, D:D.520, D:F.521 GOL.32: 7 residues within 4Å: Chain D: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.344 GOL.37: 7 residues within 4Å: Chain B: V.94 Chain E: K.2, E.24, S.27, L.29, R.30, E.233 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:E.24, E:S.27, E:R.30, E:E.233, B:V.94 Water bridges: E:E.24, E:E.24, E:E.233, E:E.233

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 8 residues within 4Å: Chain A: R.101, S.214, R.215, C.217 Chain D: R.101, S.214, R.215, C.217 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:R.215, A:C.217, D:R.215, D:C.217

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

MG.9: 2 residues within 4Å: Chain A: E.116, V.123 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, A:V.123, H2O.7, H2O.7 MG.14: 1 residues within 4Å: Chain A: D.176 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain A: E.19 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain B: D.270 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.270, H2O.29, H2O.29, H2O.29, H2O.29 MG.23: 2 residues within 4Å: Chain B: E.103, Q.420 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain C: E.29 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.29, H2O.33, H2O.34, H2O.35, H2O.38 MG.33: 1 residues within 4Å: Chain D: E.174 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.174, H2O.49, H2O.49, H2O.49 MG.39: 2 residues within 4Å: Chain E: D.270, E.273 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.270, H2O.70, H2O.70 MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain E: D.146 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.146, H2O.66, H2O.66, H2O.66 MG.42: 2 residues within 4Å: Chain F: E.29, I.30 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.29, H2O.75, H2O.75, H2O.79, H2O.79

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

NA.10: 3 residues within 4Å: Chain A: K.10, F.13, E.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.13 NA.11: 3 residues within 4Å: Chain A: R.224 Chain D: R.269 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.269 Water bridges: D:A.271 NA.12: 3 residues within 4Å: Chain A: A.543, T.546, P.547 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.546, A:T.546, A:T.546 NA.13: 4 residues within 4Å: Chain A: P.57, I.59, G.60, T.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.57 Water bridges: A:L.63 NA.19: 1 residues within 4Å: Chain B: N.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.440 NA.22: 3 residues within 4Å: Chain B: D.98, D.99, T.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.100 Water bridges: B:D.97 NA.34: 3 residues within 4Å: Chain D: K.10, F.13, E.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.10 NA.35: 3 residues within 4Å: Chain A: R.269 Chain D: R.224 Ligands: GOL.30 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Water bridges: A:V.268, D:E.274 NA.36: 4 residues within 4Å: Chain D: P.57, I.59, G.60, T.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.61 Water bridges: D:L.63

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

CL.20: 2 residues within 4Å: Chain B: R.234, A.299 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain E: R.234, A.299 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grabarse, W. et al., On the Mechanism of Biological Methane Formation: Structural Evidence for Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding. J.Mol.Biol. (2001)

Release Date

2001-08-16

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

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