- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- hetero-oligomer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
TP7.3: 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: SHT.6
21 PLIP interactions:9 interactions with chain B, 7 interactions with chain D, 5 interactions with chain A- Hydrophobic interactions: B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380, A:M.323, 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
TP7.18: 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: SHT.20
21 PLIP interactions:7 interactions with chain E, 8 interactions with chain A, 6 interactions with chain D- 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:G.368, A:K.255, A:K.255
- Salt bridges: E:H.378, A:R.224, A:K.255, A:K.255, D:R.269
- Water bridges: A:R.224, A:R.224, A:K.255, D:R.269, D:R.269, D:M.323
- 2 x F43: FACTOR 430(Non-covalent)
F43.4: 36 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.19, SHT.20
38 PLIP interactions:15 interactions with chain F, 14 interactions with chain D, 6 interactions with chain A, 3 interactions with chain E,- Hydrophobic interactions: F:L.116, 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:V.327, 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:R.119, 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
F43.17: 36 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, SHT.6
34 PLIP interactions:12 interactions with chain A, 14 interactions with chain C, 6 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: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, C:G.156, 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:R.119, C:H.155, C:H.157, C:H.157
- Salt bridges: C:H.155, C:H.157
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
COM.5: 10 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: SHT.6, F43.17
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain A- Water bridges: C:R.119, C:R.119, C:R.119, C:R.119
- Salt bridges: C:R.119
- Hydrogen bonds: A:Y.443
COM.19: 10 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, SHT.20
6 PLIP interactions:5 interactions with chain F, 1 interactions with chain D- Water bridges: F:R.119, F:R.119, F:R.119, F:R.119
- Salt bridges: F:R.119
- Hydrogen bonds: D:Y.443
- 2 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)
SHT.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.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Chain D: R.224, K.255, H.256
- Ligands: TP7.3, COM.5, F43.17
23 PLIP interactions:9 interactions with chain B, 7 interactions with chain D, 7 interactions with chain A- Hydrophobic interactions: B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380, A:M.323, A:F.329
- Hydrogen bonds: B:G.368, D:K.255, D:K.255, A:Y.332
- Water bridges: B:Y.366, B:G.368, 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
SHT.20: 22 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, V.481
- Chain E: F.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Ligands: F43.4, TP7.18, COM.19
24 PLIP interactions:11 interactions with chain E, 7 interactions with chain A, 6 interactions with chain D- Hydrophobic interactions: 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:Y.366, E:Y.366, E:G.368, A:K.255
- Water bridges: E:G.368, A:R.224, A:R.224, A:K.255, D:R.269, D:R.269, D:M.323
- Salt bridges: E:H.378, A:R.224, A:K.255, A:K.255, D:R.269
- 1 x ACT: ACETATE ION(Non-functional Binders)
- 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.11: 1 residues within 4Å:- Chain B: K.256
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.256
EDO.21: 1 residues within 4Å:- Chain D: Y.347
No protein-ligand interaction detected (PLIP)EDO.24: 4 residues within 4Å:- Chain F: R.42, G.45, E.46, E.47
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:R.42
- Water bridges: F:R.42
EDO.25: 3 residues within 4Å:- Chain F: Q.234, R.235, V.238
No protein-ligand interaction detected (PLIP)- 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 1.35 Å
- Oligo State
- hetero-oligomer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)
- 1 x ACT: ACETATE ION(Non-functional Binders)
- 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