- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- hetero-oligomer
- Ligands
- 5 x MG: MAGNESIUM ION(Non-covalent)
- 2 x F43: FACTOR 430(Non-covalent)
F43.2: 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.14
35 PLIP interactions:14 interactions with chain D, 13 interactions with chain F, 3 interactions with chain E, 5 interactions with chain A,- Hydrophobic interactions: D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442, F:L.116, F:V.154, A:I.235
- Hydrogen bonds: D:V.327, D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, F:S.117, F:G.118, F:S.153, F:V.154, E:I.365, E:Y.366, E:Y.366, A:V.144, A:V.145, A:Q.146, A:Q.229
- Water bridges: D:T.330, D:S.398, F:S.117, F:H.155, F:G.156, F:G.156, F:H.157
- Salt bridges: F:H.155, F:H.157
F43.12: 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, M.228, Q.229, M.232, A.242
- Ligands: COM.4
32 PLIP interactions:12 interactions with chain C, 6 interactions with chain D, 2 interactions with chain B, 12 interactions with chain A,- Hydrogen bonds: 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, A:V.327, A:G.328, A:Q.331, A:Q.331, A:Y.332
- Water bridges: C:S.117, C:H.155, C:G.156, C:G.156, C:H.157, D:Q.146, A:T.330, A:S.398
- Salt bridges: C:H.155, C:H.157
- Hydrophobic interactions: D:Q.146, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.442
- 2 x TP7: Coenzyme B(Non-covalent)
TP7.3: 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: XP8.5
23 PLIP interactions:10 interactions with chain B, 6 interactions with chain A, 7 interactions with chain D- Hydrophobic interactions: B:F.361, B:F.361, B:Y.366, B:Y.366, B:I.379, B:V.380, A:M.323, A:F.329, A:F.329
- Hydrogen bonds: B:G.368, D:K.255, D:K.255
- Water bridges: B:Y.366, B:G.368, A:R.269, A:M.323, D:R.224, D:R.224
- Salt bridges: B:H.378, A:R.269, D:R.224, D:K.255, D:K.255
TP7.13: 20 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.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Ligands: XP8.15
22 PLIP interactions:10 interactions with chain E, 4 interactions with chain D, 8 interactions with chain A- 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:G.368, A:K.255, A:K.255
- Water bridges: E:Y.366, E:G.368, D:R.269, 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.4: 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: XP8.5, F43.12
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.14: 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: F43.2, XP8.15
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain F- Hydrogen bonds: D:Y.443
- Water bridges: F:R.119, F:R.119
- Salt bridges: F:R.119
- 2 x XP8: O-phosphono-N-(8-sulfanyloctanoyl)-L-threonine(Non-covalent)
XP8.5: 20 residues within 4Å:- Chain A: R.269, L.319, M.323, S.324, F.329, F.442, 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: TP7.3, COM.4
21 PLIP interactions:11 interactions with chain B, 3 interactions with chain A, 7 interactions with chain D- Hydrophobic interactions: B:F.360, B:F.361, 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
- Water bridges: B:Y.366, B:G.368, A:R.269, A:M.323, D:R.224, D:R.224
- Salt bridges: B:H.378, A:R.269, D:R.224, D:K.255, D:K.255
XP8.15: 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, V.481
- Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Ligands: TP7.13, COM.14
23 PLIP interactions:11 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:M.323, D:V.481
- Hydrogen bonds: E:G.368, A:K.255, A:K.255
- Water bridges: E:Y.366, E:G.368, D:R.269, 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
- 1 x ACT: ACETATE ION(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 6 residues within 4Å:- Chain A: D.514, D.515, L.517, V.518, F.519, D.520
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.517
- Water bridges: A:F.521
EDO.8: 1 residues within 4Å:- Chain A: Y.347
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.347
EDO.16: 6 residues within 4Å:- Chain D: K.21
- Chain F: R.146, E.163, D.164, G.165, E.206
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain D- Hydrogen bonds: F:R.146, D:K.21
EDO.17: 1 residues within 4Å:- Chain D: Y.347
No protein-ligand interaction detected (PLIP)- 1 x ZN: ZINC ION(Non-covalent)
- 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 1.80 Å
- Oligo State
- hetero-oligomer
- Ligands
- 5 x MG: MAGNESIUM ION(Non-covalent)
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x XP8: O-phosphono-N-(8-sulfanyloctanoyl)-L-threonine(Non-covalent)
- 1 x ACT: ACETATE ION(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 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