SMTL ID : 3m2u.1

Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-oligomer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: K.530 Ligands: ACT.7 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: E.19 No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: D.270 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.270, H2O.23, H2O.24, H2O.27, H2O.32, H2O.35 MG.14: 2 residues within 4Å: Chain C: E.29, K.134 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.29, H2O.39, H2O.43, H2O.43, H2O.43, H2O.43 MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 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.63, H2O.63, H2O.64 MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain E: D.270 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.270, H2O.73, H2O.74, H2O.77, H2O.79 MG.29: 1 residues within 4Å: Chain F: E.29 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.29, H2O.83, H2O.86, H2O.86, H2O.87, H2O.87

2 x F43: FACTOR 430(Non-covalent)

F43.3: 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.23 38 PLIP interactions: 12 interactions with chain D, 16 interactions with chain F, 6 interactions with chain A, 3 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.442, F:L.116, A:Q.146, A:I.235 Hydrogen bonds: D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, F:S.117, F:G.118, F:R.119, F:S.153, F:V.154, F:G.156, A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366 Water bridges: D:T.330, D:S.398, F:S.117, F:G.118, F:R.119, F:H.155, F:H.157, F:H.157, F:H.157 Salt bridges: F:H.155, F:H.157 Metal complexes: H2O.19 F43.21: 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.5 36 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B, 6 interactions with chain D, 14 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442, D:Q.146, D:I.235, C:L.116 Hydrogen bonds: A:V.327, A:G.328, A:Q.331, A:Q.331, A:Y.332, B:I.365, B:Y.366, D:V.144, D:V.145, D:Q.146, D:Q.229, C:S.117, C:G.118, C:R.119, C:S.153, C:V.154 Water bridges: A:T.330, A:S.398, C:S.117, C:R.119, C:H.155, C:G.156, C:G.156, C:H.157 Salt bridges: C:H.155, C:H.157 Metal complexes: H2O.19

2 x TP7: COENZYME B(Non-covalent)

TP7.4: 21 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, I.379, V.380 Chain D: R.224, K.255, H.256 Ligands: TXZ.6 22 PLIP interactions: 10 interactions with chain B, 6 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: B:F.360, B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380, A:M.323, A:F.329 Hydrogen bonds: B:Y.366, B:G.368, D:K.255 Water bridges: B:Y.366, D:R.224, D:R.224, A:R.269, A:R.269, A:M.323 Salt bridges: B:H.378, D:R.224, D:K.255, D:K.255, A:R.269 TP7.22: 21 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, I.379, V.380 Ligands: TXZ.24 23 PLIP interactions: 10 interactions with chain E, 5 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: E:F.360, E:F.361, E:F.361, E:Y.366, E:Y.366, E:I.379, E:V.380, D:M.323, D:F.329 Hydrogen bonds: E:G.368, A:K.255, A:K.255 Water bridges: E:G.368, D:R.269, D:M.323, A:R.224, A:R.224, A:K.255 Salt bridges: E:H.378, D:R.269, A:R.224, A:K.255, A:K.255

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

COM.5: 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: F43.21 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Y.443 Water bridges: C:R.119, C:R.119, C:R.119 Salt bridges: C:R.119 COM.23: 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: F43.3 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:Y.443 Water bridges: F:R.119, F:R.119, F:R.119, F:R.119 Salt bridges: F:R.119

2 x TXZ: O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE(Non-covalent)

TXZ.6: 20 residues within 4Å: Chain A: R.269, 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, I.379, V.380 Chain D: R.224, K.255, H.256 Ligands: TP7.4 18 PLIP interactions: 8 interactions with chain B, 6 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380, A:F.329 Hydrogen bonds: B:Y.366, B:G.368, D:K.255 Salt bridges: B:H.378, D:R.224, D:K.255, D:K.255, A:R.269 Water bridges: D:R.224, D:R.224, A:R.269, A:R.269 TXZ.24: 20 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, 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, I.379, V.380 Ligands: TP7.22 19 PLIP interactions: 9 interactions with chain E, 4 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380, D:M.323, D:F.329 Hydrogen bonds: E:Y.366, E:G.368, A:K.255 Water bridges: E:G.368, D:R.269, A:R.224, A:R.224 Salt bridges: E:H.378, D:R.269, A:R.224, A:K.255, A:K.255

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: V.518, K.530, E.535, F.536, E.537 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.536 Hydrogen bonds: A:E.537 Water bridges: A:E.527, A:E.527, A:K.530, A:K.530, A:K.530 Salt bridges: A:K.530 ACT.15: 4 residues within 4Å: Chain A: G.60, T.61, P.62 Chain C: K.152 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:G.191, C:D.192 Salt bridges: C:K.152 Hydrophobic interactions: A:T.61

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 1 residues within 4Å: Chain A: Y.347 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: N.109, H.110, E.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.109 EDO.16: 2 residues within 4Å: Chain C: R.235, V.238 No protein-ligand interaction detected (PLIP) EDO.25: 1 residues within 4Å: Chain D: Y.347 No protein-ligand interaction detected (PLIP) EDO.26: 6 residues within 4Å: Chain D: K.21 Chain F: R.146, E.163, D.164, G.165, E.206 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:K.21, F:R.146 Water bridges: F:D.164 EDO.30: 2 residues within 4Å: Chain F: K.131, I.132 No protein-ligand interaction detected (PLIP) EDO.31: 1 residues within 4Å: Chain F: R.235 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 2 residues within 4Å: Chain A: A.47, G.51 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.48, A:Q.54 PEG.17: 5 residues within 4Å: Chain C: R.42, G.45, E.46, E.47, Y.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.42

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 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 D, 2 interactions with chain A Metal complexes: D:R.215, D:C.217, A:R.215, A:C.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cedervall, P.E. et al., Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues. Biochemistry (2010)

Release Date

2010-09-15

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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