SMTL ID : 1hbm.1

METHYL-COENZYME M REDUCTASE ENZYME PRODUCT COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-oligomer

Ligands

2 x F43: FACTOR 430(Non-covalent)

F43.1: 34 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, Q.229, M.232, I.235, A.242 Ligands: SHT.2 33 PLIP interactions: 12 interactions with chain A, 14 interactions with chain C, 5 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442, C:L.116, D:I.235 Hydrogen bonds: A:G.328, A:Q.331, A:Q.331, A:Y.332, 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, B:I.365, B:Y.366 Water bridges: A:T.330, A:S.398, C:S.117, C:H.155, C:H.155, C:G.156, C:G.156, C:H.157 Salt bridges: C:H.155, C:H.157 F43.17: 33 residues within 4Å: Chain A: A.143, V.144, V.145, Q.146, M.149, Q.229, M.232, 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: SHT.18 37 PLIP interactions: 13 interactions with chain F, 7 interactions with chain A, 14 interactions with chain D, 3 interactions with chain E, Hydrogen bonds: F:S.117, F:G.118, F:S.153, F:V.154, F:G.156, A:V.144, A:V.145, A:Q.146, A:Q.229, D:V.327, D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, E:I.365, E:Y.366, E:Y.366 Water bridges: F:S.117, F:H.155, F:H.155, F:H.157, F:H.157, F:H.157, A:A.242, D:T.330, D:S.398 Salt bridges: F:H.155, F:H.157 Hydrophobic interactions: A:Q.146, A:A.242, D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442

2 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)

SHT.2: 23 residues within 4Å: Chain A: R.269, L.319, M.323, S.324, F.329, Y.332, F.442, M.479, N.480, V.481 Chain B: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.224, K.255, H.256 Ligands: F43.1, GOL.20 21 PLIP interactions: 6 interactions with chain A, 7 interactions with chain D, 8 interactions with chain B Hydrophobic interactions: A:M.323, A:F.329, B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380 Hydrogen bonds: A:Y.332, D:K.255, D:K.255, B:G.368 Water bridges: A:M.323, A:Y.443, D:R.224, D:R.224, B:Y.366 Salt bridges: A:R.269, D:R.224, D:K.255, D:K.255, B:H.378 SHT.18: 23 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, L.319, M.323, S.324, F.329, Y.332, F.442, M.479, N.480, V.481 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Ligands: GOL.3, F43.17 19 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A, 8 interactions with chain E Hydrophobic interactions: D:M.323, D:F.329, E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380 Water bridges: D:Y.443, A:R.224, A:R.224 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:Y.366, E:G.368

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.223, K.255, H.256, H.261, E.274 Chain D: R.269 Ligands: SHT.18, NA.25 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.224, A:E.274 Water bridges: A:R.224, A:R.224, A:R.224, A:E.274 GOL.4: 6 residues within 4Å: Chain A: D.169, A.172, D.173, V.180, D.182, N.184 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.173, A:D.182, A:N.184 Water bridges: A:D.182, A:D.182, A:I.183 GOL.5: 5 residues within 4Å: Chain A: V.518, K.530, E.535, F.536, E.537 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.530, A:K.530, A:E.537 Water bridges: A:E.527, A:K.530 GOL.6: 7 residues within 4Å: Chain A: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.3 Water bridges: A:A.1, A:D.2 GOL.11: 6 residues within 4Å: Chain B: K.2, E.24, S.27, R.30, E.233 Chain E: V.94 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:E.24, B:S.27, B:R.30, E:V.94 Water bridges: B:E.233 GOL.15: 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.19: 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.20: 8 residues within 4Å: Chain D: S.223, R.224, K.255, H.256, H.261, E.274 Ligands: SHT.2, NA.8 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain D Water bridges: A:R.269, D:R.224, D:R.224, D:R.224, D:E.274, D:E.274, D:E.274 Hydrogen bonds: D:S.223, D:S.223, D:K.255 GOL.21: 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 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.293, D:D.514, D:L.517, D:F.521 GOL.22: 7 residues within 4Å: Chain D: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379 No protein-ligand interaction detected (PLIP) GOL.27: 6 residues within 4Å: Chain B: V.94 Chain E: K.2, E.24, S.27, R.30, E.233 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:E.24, E:S.27, E:S.27, E:R.30, B:V.94 Water bridges: E:E.24, E:E.24, E:E.233

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

NA.7: 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.8: 2 residues within 4Å: Chain A: R.269 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.269 Water bridges: A:A.271 NA.9: 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.10: 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.12: 1 residues within 4Å: Chain B: N.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.440 NA.14: 4 residues within 4Å: Chain B: D.98, D.99, T.100, N.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.98 Water bridges: B:D.97 NA.24: 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.25: 2 residues within 4Å: Chain D: R.269 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.269 Water bridges: D:A.271 NA.26: 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.13: 2 residues within 4Å: Chain B: R.234, A.299 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain E: R.234, A.299 Ligand excluded by PLIP

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

MG.16: 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.32, H2O.33, H2O.33, H2O.37 MG.29: 1 residues within 4Å: Chain F: E.29 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.29, H2O.72, H2O.73, H2O.73, H2O.77 MG.30: 1 residues within 4Å: Chain E: D.76 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.23: 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

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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