- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.16 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: 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: GOL.32
19 PLIP interactions:4 interactions with chain A, 8 interactions with chain B, 7 interactions with chain D- 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, B:G.368, D:R.224, D:R.224
- Salt bridges: A:R.269, B:H.378, D:R.224, D:K.255, D:K.255
- Hydrogen bonds: B:G.368, D:K.255, D:K.255
TP7.29: 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
22 PLIP interactions:9 interactions with chain E, 5 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: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.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.30: 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: F43.28
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
- 11 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: S.223, R.224, K.255, H.256, H.261, E.274
- Ligands: NA.11
9 PLIP interactions:8 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:S.223, A:S.223, A:R.224
- Water bridges: A:R.224, A:R.224, A:R.224, A:E.274, A:E.274, D:R.269
GOL.5: 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.6: 5 residues within 4Å:- Chain A: V.518, K.530, E.535, F.536, E.537
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:K.530, A:K.530, A:E.537, A:E.537
- Water bridges: A:E.527, A:K.530
GOL.7: 5 residues within 4Å:- Chain A: K.3, D.344, Y.347, 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.19: 7 residues within 4Å:- Chain B: K.2, E.24, S.27, L.29, 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.25: 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.31: 6 residues within 4Å:- Chain D: D.169, A.172, D.173, V.180, 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.32: 8 residues within 4Å:- Chain D: S.223, R.224, K.255, H.256, H.261, E.274
- Ligands: TP7.2, NA.38
10 PLIP interactions:1 interactions with chain A, 9 interactions with chain D- Water bridges: A:R.269, D:R.224, D:R.224, D:R.224, D:E.274, D:E.274, D:E.274
- Hydrogen bonds: D:S.223, D:S.223, D:K.255
GOL.33: 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
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:Q.290, D:R.293, D:F.512, D:D.514, D:F.521
GOL.34: 6 residues within 4Å:- Chain D: K.3, L.4, D.344, Y.347, E.351, Y.379
No protein-ligand interaction detected (PLIP)GOL.40: 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:E.24, E:E.24
- 1 x ZN: ZINC ION(Non-covalent)
- 18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.9: 2 residues within 4Å:- Chain A: E.116, V.123
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.116, A:V.123, H2O.8, H2O.8
MG.14: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.15: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.16: 1 residues within 4Å:- Chain A: E.19
No protein-ligand interaction detected (PLIP)MG.17: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.22: 1 residues within 4Å:- Chain B: D.270
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.270, H2O.31, H2O.31, H2O.31, H2O.31
MG.24: 1 residues within 4Å:- Chain B: E.103
No protein-ligand interaction detected (PLIP)MG.26: 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.38, H2O.38, H2O.42, H2O.42
MG.27: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.35: 1 residues within 4Å:- Chain D: E.174
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:E.174, H2O.52, H2O.55, H2O.56, H2O.56
MG.36: 1 residues within 4Å:- Chain D: D.355
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:D.355
MG.42: 1 residues within 4Å:- Chain E: D.270
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:D.270, H2O.78, H2O.78, H2O.78
MG.43: 1 residues within 4Å:- Chain E: D.146
5 PLIP interactions:1 interactions with chain E, 4 Ligand-Water interactions- Metal complexes: E:D.146, H2O.70, H2O.74, H2O.74, H2O.74
MG.44: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.45: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.46: 1 residues within 4Å:- Chain E: K.89
No protein-ligand interaction detected (PLIP)MG.47: 1 residues within 4Å:- Chain F: E.29
5 PLIP interactions:1 interactions with chain F, 4 Ligand-Water interactions- Metal complexes: F:E.29, H2O.83, H2O.84, H2O.84, H2O.88
MG.48: 3 residues within 4Å:- Chain F: E.33, D.34, K.37
3 PLIP interactions:2 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:E.33, F:D.34, H2O.84
- 10 x NA: SODIUM ION(Non-functional Binders)
NA.10: 3 residues within 4Å:- Chain A: K.10, F.13, E.14
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.14
NA.11: 3 residues within 4Å:- Chain A: R.224
- Chain D: R.269
- Ligands: GOL.4
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain A- Water bridges: D:V.268, D:A.271, A:E.274
NA.12: 4 residues within 4Å:- Chain A: A.543, T.546, P.547, A.548
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.543, A:T.546, A:T.546
NA.13: 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.18: 0 residues within 4Å:- (No contacts)
3 PLIP interactions:3 interactions with chain A- Water bridges: A:E.386, A:E.386, A:E.386
NA.20: 1 residues within 4Å:- Chain B: N.440
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.440
NA.23: 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.97
NA.37: 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.38: 3 residues within 4Å:- Chain A: R.269
- Chain D: R.224
- Ligands: GOL.32
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.269
- Water bridges: A:A.271
NA.39: 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:P.57
- Water bridges: D:L.63
- 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 1.16 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)
- 11 x GOL: GLYCEROL(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 10 x NA: SODIUM ION(Non-functional Binders)
- 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