- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- hetero-oligomer
- Ligands
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)
SHT.2: 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: F43.1, GOL.20
21 PLIP interactions:6 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
- Hydrogen bonds: A:Y.332, D:K.255, D:K.255, B:G.368
- Water bridges: A:M.323, A:Y.443, D:R.224, D:R.224, B:Y.366
- Salt bridges: A:R.269, D:R.224, D:K.255, D:K.255, B:H.378
SHT.18: 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: GOL.3, F43.17
19 PLIP interactions:4 interactions with chain D, 7 interactions with chain A, 8 interactions with chain E- Hydrophobic interactions: D:M.323, D:F.329, E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380
- Water bridges: D:Y.443, A:R.224, A:R.224
- Salt bridges: D:R.269, A:R.224, A:K.255, A:K.255, E:H.378
- Hydrogen bonds: A:K.255, A:K.255, E:Y.366, E:G.368
- 11 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 8 residues within 4Å:- Chain A: S.223, K.255, H.256, H.261, E.274
- Chain D: R.269
- Ligands: SHT.18, NA.25
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.224, A:E.274
- Water bridges: A:R.224, A:R.224, A:R.224, A:E.274
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: 7 residues within 4Å:- Chain A: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.3
- Water bridges: A:A.1, A:D.2
GOL.11: 6 residues within 4Å:- Chain B: K.2, E.24, S.27, R.30, E.233
- Chain E: V.94
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain E- Hydrogen bonds: B:E.24, B:S.27, B:R.30, E:V.94
- Water bridges: B:E.233
GOL.15: 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.19: 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.20: 8 residues within 4Å:- Chain D: S.223, R.224, K.255, H.256, H.261, E.274
- Ligands: SHT.2, NA.8
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.21: 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:D.514, D:L.517, D:F.521
GOL.22: 7 residues within 4Å:- Chain D: K.3, L.4, D.344, Y.347, F.348, E.351, Y.379
No protein-ligand interaction detected (PLIP)GOL.27: 6 residues within 4Å:- Chain B: V.94
- Chain E: K.2, E.24, S.27, R.30, E.233
8 PLIP interactions:7 interactions with chain E, 1 interactions with chain B- Hydrogen bonds: E:E.24, E:S.27, E:S.27, E:R.30, B:V.94
- Water bridges: E:E.24, E:E.24, E:E.233
- 9 x NA: SODIUM ION(Non-functional Binders)
NA.7: 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.8: 2 residues within 4Å:- Chain A: R.269
- Ligands: GOL.20
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.269
- Water bridges: A:A.271
NA.9: 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.10: 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.12: 1 residues within 4Å:- Chain B: N.440
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.440
NA.14: 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:D.98
- Water bridges: B:D.97
NA.24: 3 residues within 4Å:- Chain D: K.10, F.13, E.14
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.10
NA.25: 2 residues within 4Å:- Chain D: R.269
- Ligands: GOL.3
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:R.269
- Water bridges: D:A.271
NA.26: 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
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.16: 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.32, H2O.33, H2O.33, H2O.37
MG.29: 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.72, H2O.73, H2O.73, H2O.77
MG.30: 1 residues within 4Å:- Chain E: D.76
No protein-ligand interaction detected (PLIP)MG.31: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.32: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 1 x ZN: ZINC ION(Non-covalent)
- 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 1.80 Å
- Oligo State
- hetero-oligomer
- Ligands
- 2 x F43: FACTOR 430(Non-covalent)
- 2 x SHT: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE(Non-covalent)
- 11 x GOL: GLYCEROL(Non-functional Binders)
- 9 x NA: SODIUM ION(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 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