- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.78 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
TP7.2: 19 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
20 PLIP interactions:4 interactions with chain A, 7 interactions with chain D, 9 interactions with chain B- Hydrophobic interactions: A:M.323, A:F.329, B:F.361, B:Y.366, B:I.379, B:V.380
- Water bridges: A:M.323, D:R.224, D:R.224, B:Y.366, B:G.368, B:H.378
- 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
TP7.21: 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.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380
20 PLIP interactions:9 interactions with chain E, 4 interactions with chain D, 7 interactions with chain A- Hydrophobic interactions: E:F.360, E:F.361, E:Y.366, E:I.379, E:V.380, D:L.319, D:M.323, D:F.329
- Hydrogen bonds: E:G.368, A:K.255, A:K.255
- Water bridges: E:G.368, E:H.378, A:R.224, A:R.224
- 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.3: 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: F43.1
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.22: 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: F43.20
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
- 9 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 6 residues within 4Å:- Chain A: D.169, A.172, D.173, V.180, D.182, N.184
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:D.173, A:D.182, A:N.184
- Water bridges: A:D.182, A:D.182, A:I.183
GOL.5: 5 residues within 4Å:- Chain A: V.518, K.530, E.535, F.536, E.537
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.530, A:K.530, A:E.537
- Water bridges: A:E.527, A:K.530
GOL.6: 6 residues within 4Å:- Chain A: K.3, D.344, Y.347, F.348, E.351, Y.379
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.379
- Water bridges: A:A.1, A:A.1, A:D.2, A:K.3
GOL.14: 6 residues within 4Å:- Chain B: K.2, E.24, S.27, R.30, E.233
- Chain E: V.94
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain E- Hydrogen bonds: B:S.27, B:R.30, E:V.94
GOL.18: 6 residues within 4Å:- Chain C: I.72, Y.108, R.109, D.128, K.131, I.132
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.109, C:D.128, C:D.128
GOL.23: 5 residues within 4Å:- Chain D: D.169, A.172, D.173, D.182, N.184
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:D.173, D:D.182, D:N.184
- Water bridges: D:D.182, D:D.182, D:I.183
GOL.24: 11 residues within 4Å:- Chain D: Q.290, R.293, F.512, A.513, D.514, D.515, L.517, F.519, D.520, F.521, T.522
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.293, D:R.293, D:D.514, D:F.521
GOL.25: 6 residues within 4Å:- Chain D: K.3, D.344, Y.347, F.348, E.351, Y.379
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:E.351
- Water bridges: D:A.1, D:D.2
GOL.28: 7 residues within 4Å:- Chain B: V.94
- Chain E: K.2, E.24, S.27, L.29, R.30, E.233
7 PLIP interactions:6 interactions with chain E, 1 interactions with chain B- Hydrogen bonds: E:E.24, E:S.27, E:R.30, E:E.233, B:V.94
- Water bridges: E:K.2, E:E.24
- 1 x ZN: ZINC ION(Non-covalent)
- 8 x NA: SODIUM ION(Non-functional Binders)
NA.8: 3 residues within 4Å:- Chain A: K.10, F.13, E.14
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:F.13
NA.9: 2 residues within 4Å:- Chain A: R.269
- Chain D: R.224
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.269
- Water bridges: A:A.271
NA.10: 3 residues within 4Å:- Chain A: A.543, T.546, P.547
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.546, A:T.546, A:T.546
NA.11: 4 residues within 4Å:- Chain A: P.57, I.59, G.60, T.61
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:P.57
- Water bridges: A:L.63
NA.15: 1 residues within 4Å:- Chain B: N.440
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.440
NA.17: 4 residues within 4Å:- Chain B: D.98, D.99, T.100, N.101
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.100
- Water bridges: B:D.98
NA.26: 3 residues within 4Å:- Chain D: K.10, F.13, E.14
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:E.14
NA.27: 4 residues within 4Å:- Chain D: P.57, I.59, G.60, T.61
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:T.61
- Water bridges: D:L.63
- 4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.12: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.13: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.19: 1 residues within 4Å:- Chain C: E.29
5 PLIP interactions:1 interactions with chain C, 4 Ligand-Water interactions- Metal complexes: C:E.29, H2O.33, H2O.34, H2O.34, H2O.38
MG.30: 2 residues within 4Å:- Chain F: E.29, I.30
5 PLIP interactions:1 interactions with chain F, 4 Ligand-Water interactions- Metal complexes: F:E.29, H2O.73, H2O.74, H2O.74, H2O.77
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Grabarse, W. et al., On the Mechanism of Biological Methane Formation: Structural Evidence for Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding. J.Mol.Biol. (2001)
- Release Date
- 2001-08-16
- Peptides
- METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT: AD
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT: BE
METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.78 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x TP7: Coenzyme B(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 9 x GOL: GLYCEROL(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 8 x NA: SODIUM ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Grabarse, W. et al., On the Mechanism of Biological Methane Formation: Structural Evidence for Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding. J.Mol.Biol. (2001)
- Release Date
- 2001-08-16
- Peptides
- METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT: AD
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT: BE
METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F