- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.45 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 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.21
38 PLIP interactions:7 interactions with chain A, 15 interactions with chain F, 13 interactions with chain D, 3 interactions with chain E,- Hydrophobic interactions: A:Q.146, A:I.235, F:L.116, F:V.154, D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442
- Hydrogen bonds: A:V.144, A:V.145, A:Q.146, A:Q.229, 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, E:I.365, E:Y.366, E:Y.366
- Water bridges: A:Q.146, F:S.117, 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
F43.19: 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 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
35 PLIP interactions:14 interactions with chain C, 12 interactions with chain A, 7 interactions with chain D, 2 interactions with chain B,- Hydrophobic interactions: C:L.116, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442, D:Q.146, D:I.235
- Hydrogen bonds: C:S.117, C:G.118, C:R.119, C:S.153, C:V.154, A:G.328, A:Q.331, A:Q.331, A:Y.332, D:V.144, D:V.145, D:Q.146, D:Q.229, B:I.365, B:Y.366
- Water bridges: C:S.117, C:H.155, C:H.155, C:G.156, C:G.156, C:H.157, A:T.330, A:S.398, D:Q.146
- Salt bridges: C:H.155, C:H.157
- 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
19 PLIP interactions:4 interactions with chain A, 7 interactions with chain D, 8 interactions with chain B- Hydrophobic interactions: A:M.323, A:F.329, B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380
- Water bridges: A:R.269, D:R.224, D:R.224, B:G.368
- Salt bridges: A:R.269, D:R.224, D:K.255, D:K.255, B:H.378
- Hydrogen bonds: D:K.255, D:K.255, B:G.368
TP7.20: 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: XP9.22
20 PLIP interactions:7 interactions with chain A, 4 interactions with chain D, 9 interactions with chain E- Hydrogen bonds: A:K.255, A:K.255, E:G.368
- Water bridges: A:R.224, A:R.224, D:R.269, E:G.368
- Salt bridges: A:R.224, A:K.255, A:K.255, D:R.269, E:H.378
- Hydrophobic interactions: D:M.323, D:F.329, E:F.360, E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380
- 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: XP9.6, F43.19
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Water bridges: C:R.119, C:R.119
- Salt bridges: C:R.119
- Hydrogen bonds: A:Y.443
COM.21: 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: F43.3, XP9.22
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 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
22 PLIP interactions:5 interactions with chain A, 7 interactions with chain D, 10 interactions with chain B- 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
- Water bridges: A:R.269, A:M.323, D:R.224, D:R.224, B:Y.366, B:G.368
- Salt bridges: A:R.269, D:R.224, D:K.255, D:K.255, B:H.378
- Hydrogen bonds: D:K.255, D:K.255, B:G.368
XP9.22: 23 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, N.480, V.481
- Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380
- Ligands: TP7.20, COM.21
22 PLIP interactions:8 interactions with chain A, 5 interactions with chain D, 9 interactions with chain E- Hydrogen bonds: A:K.255, A:K.255, E:G.368
- Water bridges: A:R.224, A:R.224, A:K.255, D:R.269, D:M.323, E:G.368
- Salt bridges: A:R.224, A:K.255, A:K.255, D:R.269, E:H.378
- Hydrophobic interactions: D:F.329, D:F.442, E:F.360, E:F.361, E:Y.366, E:Y.366, E:I.379, E:V.380
- 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
- Water bridges: A:K.530, A:K.530, A:K.530
- Salt bridges: 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
- Water bridges: C:S.50
- Hydrogen bonds: D:R.118
- 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)
- 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 1.45 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 9 x MG: MAGNESIUM ION(Non-functional Binders)(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 XP9: O-phosphono-N-(9-sulfanylnonanoyl)-L-threonine(Non-covalent)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 6 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