- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- hetero-oligomer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 2 x F43: FACTOR 430(Non-covalent)
F43.4: 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.18
38 PLIP interactions:16 interactions with chain F, 13 interactions with chain D, 6 interactions with chain A, 3 interactions with chain E,- Hydrophobic interactions: F:L.116, F:V.154, D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442, A:Q.146, A:I.235
- Hydrogen bonds: F:S.117, F:G.118, F:R.119, F:S.153, F:V.154, F:G.156, 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
- Water bridges: F:S.117, F:G.118, F:H.155, F:H.157, F:H.157, F:H.157, D:T.330, D:S.398
- Salt bridges: F:H.155, F:H.157
F43.16: 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.6
32 PLIP interactions:6 interactions with chain D, 13 interactions with chain C, 11 interactions with chain A, 2 interactions with chain B,- Hydrophobic interactions: D:Q.146, D:I.235, C:L.116, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.442
- Hydrogen bonds: 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, C:G.156, A:G.328, 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.157, C:H.157, A:T.330, A:S.398
- Salt bridges: C:H.155, C:H.157
- 2 x TP7: Coenzyme B(Non-covalent)
TP7.5: 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: TPZ.7
22 PLIP interactions:11 interactions with chain B, 7 interactions with chain D, 4 interactions with chain A- Hydrophobic interactions: B:F.360, B:F.361, B:F.361, B:Y.366, B:Y.366, B:I.379, B:V.380, A:F.329
- Hydrogen bonds: B:G.368, D:K.255, D:K.255
- Water bridges: B:Y.366, B:G.368, D:R.224, D:R.224, A:R.269, A:M.323
- Salt bridges: B:H.378, D:R.224, D:K.255, D:K.255, A:R.269
TP7.17: 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: TPZ.19
22 PLIP interactions:10 interactions with chain E, 4 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: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.6: 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: F43.16
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.18: 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: F43.4
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
- 2 x TPZ: O-phosphono-N-(5-sulfanylpentanoyl)-L-threonine(Non-covalent)
TPZ.7: 18 residues within 4Å:- Chain A: R.269, L.319, M.323, S.324, F.329, M.479
- 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: TP7.5
17 PLIP interactions:7 interactions with chain B, 7 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: B:F.361, B:F.361, B:I.379, B:V.380, A:M.323
- Hydrogen bonds: B:G.368, D:K.255, D:K.255
- Water bridges: B:G.368, D:R.224, D:R.224, A:R.269
- Salt bridges: B:H.378, D:R.224, D:K.255, D:K.255, A:R.269
TPZ.19: 18 residues within 4Å:- Chain A: R.224, K.255, H.256
- Chain D: R.269, L.319, M.323, S.324, F.329, M.479
- Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Ligands: TP7.17
17 PLIP interactions:7 interactions with chain E, 3 interactions with chain D, 7 interactions with chain A- Hydrophobic interactions: E:F.361, E:F.361, E:I.379, E:V.380, D:M.323
- Hydrogen bonds: E:G.368, A:K.255, 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
- 5 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: 2 residues within 4Å:- Chain C: R.235, V.238
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.235
EDO.20: 1 residues within 4Å:- Chain D: Y.347
No protein-ligand interaction detected (PLIP)EDO.23: 3 residues within 4Å:- Chain F: Q.234, R.235, V.238
No protein-ligand interaction detected (PLIP)EDO.24: 4 residues within 4Å:- Chain F: R.42, G.45, E.46, E.47
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:R.42
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- hetero-oligomer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x TPZ: O-phosphono-N-(5-sulfanylpentanoyl)-L-threonine(Non-covalent)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
AD
DB
BE
EC
CF
F