SMTL ID : 3m30.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-oligomer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: MG.2 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: K.530 Ligands: MG.1, ACT.7 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 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.8122, H2O.8122, H2O.8122, H2O.8122, H2O.8122 MG.13: 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.8127, H2O.8127, H2O.8127, H2O.8127, H2O.8127 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain F: E.29 6 PLIP interactions: 5 Ligand-Water interactions, 1 interactions with chain F Metal complexes: H2O.7509, H2O.7509, H2O.7509, H2O.7509, H2O.7509, F:E.29

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 E: S.364, I.365, Y.366 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 Ligands: COM.21 Chain F: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 38 PLIP interactions: 6 interactions with chain A, 3 interactions with chain E, 13 interactions with chain D, 16 interactions with chain F Hydrophobic interactions: A:Q.146, A:I.235, D:V.327, D:F.329, D:Y.332, D:F.395, D:F.442, F:L.116, F:V.154 Hydrogen bonds: A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366, 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 Salt bridges: F:H.155, F:H.157 Water bridges: D:T.330, D:S.398, F:S.117, F:G.118, F:H.155, F:H.157, F:H.157, F:H.157 pi-Stacking: D:Y.332 F43.19: 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 C: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, H.157 Chain B: S.364, I.365, Y.366 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 33 PLIP interactions: 11 interactions with chain A, 14 interactions with chain C, 2 interactions with chain B, 6 interactions with chain D, Hydrophobic interactions: A:V.327, A:F.329, A:Y.332, A:F.395, A:F.442, C:L.116, D:Q.146, 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, B:I.365, B:Y.366, D:V.144, D:V.145, D:Q.146, D:Q.229 Salt bridges: C:H.155, C:H.157 Water bridges: A:T.330, C:S.117, C:S.117, C:H.155, C:G.156, C:G.156, C:H.157 pi-Stacking: A:Y.332

2 x TP7: Coenzyme B(Non-covalent)

TP7.4: 20 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.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.224, K.255, H.256 Ligands: XP9.6 20 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B, 8 interactions with chain D 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: B:G.368, D:K.255, D:K.255 Salt bridges: A:R.269, B:H.378, D:R.224, D:K.255, D:K.255 Water bridges: A:M.323, B:H.378, D:R.224, D:R.224, D:K.255 TP7.20: 21 residues within 4Å: Chain A: R.224, K.255, H.256 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Ligands: XP9.22 20 PLIP interactions: 7 interactions with chain A, 9 interactions with chain E, 4 interactions with chain D Hydrogen bonds: A:K.255, A:K.255, E:G.368 Hydrophobic interactions: E:F.360, E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380, D:M.323, D:F.329 Salt bridges: A:R.224, A:K.255, A:K.255, E:H.378, D:R.269 Water bridges: A:R.224, A:K.255, E:H.378, D:M.323

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

COM.5: 10 residues within 4Å: Chain A: Y.332, F.442, Y.443 Chain C: L.116, R.119 Chain B: F.360, S.364, Y.366 Ligands: XP9.6, F43.19 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.443 Salt bridges: C:R.119 Water bridges: C:R.119, C:R.119 COM.21: 10 residues within 4Å: Chain E: F.360, S.364, Y.366 Chain D: Y.332, F.442, Y.443 Ligands: F43.3, XP9.22 Chain F: L.116, R.119 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:Y.443 Salt bridges: F:R.119 Water bridges: F:R.119, F:R.119

2 x XP9: O-phosphono-N-(9-sulfanylnonanoyl)-L-threonine(Non-covalent)

XP9.6: 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: TP7.4, COM.5 19 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: A:F.329, A:F.442, B:F.360, B:F.361, B:Y.366, B:Y.366, B:I.379, B:V.380 Hydrogen bonds: B:G.368, D:K.255, D:K.255 Salt bridges: A:R.269, B:H.378, D:R.224, D:K.255, D:K.255 Water bridges: B:H.378, D:R.224, D:R.224 XP9.22: 23 residues within 4Å: Chain A: R.224, K.255, H.256 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.269, L.319, M.323, S.324, F.329, Y.332, F.442, M.479, N.480, V.481 Ligands: TP7.20, COM.21 18 PLIP interactions: 6 interactions with chain A, 9 interactions with chain E, 3 interactions with chain D Hydrogen bonds: A:K.255, A:K.255, E:G.368 Hydrophobic interactions: E:F.360, E:F.361, E:Y.366, E:Y.366, E:I.379, E:V.380, D:F.329, D:F.442 Salt bridges: A:R.224, A:K.255, A:K.255, E:H.378, D:R.269 Water bridges: A:R.224, E:H.378

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.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.536 Hydrogen bonds: A:E.537 Salt bridges: A:K.530 Water bridges: A:K.530, A:K.530, A:K.530 ACT.14: 8 residues within 4Å: Chain C: P.49, S.50, V.51, R.80 Chain D: E.116, K.117, R.118, G.120 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.49, C:R.80 Hydrogen bonds: D:R.118 Water bridges: C:S.50

6 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.12: 1 residues within 4Å: Chain B: K.256 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain C: R.235, V.238 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.235 EDO.23: 1 residues within 4Å: Chain D: Y.347 No protein-ligand interaction detected (PLIP) EDO.26: 3 residues within 4Å: Chain F: Q.234, R.235, V.238 No protein-ligand interaction detected (PLIP) EDO.27: 3 residues within 4Å: Chain F: K.131, I.132, E.135 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.135

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 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

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

PEG.16: 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

Links

RCSB   PDBe   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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