- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x RET: RETINAL(Covalent)
RET.5: 16 residues within 4Å:- Chain A: E.114, A.118, T.119, G.122, E.123, C.188, G.189, I.190, Y.192, M.208, F.213, F.262, W.266, Y.269, A.293, K.297
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:A.118, A:T.119, A:I.190, A:F.213, A:F.262, A:W.266, A:Y.269, A:Y.269, A:K.297
RET.17: 17 residues within 4Å:- Chain B: E.114, A.118, T.119, G.122, E.123, S.187, C.188, G.189, I.190, Y.192, M.208, F.213, F.262, W.266, Y.269, A.293, K.297
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:A.118, B:I.190, B:F.213, B:F.262, B:W.266, B:Y.269, B:Y.269, B:K.297
- 4 x PLM: PALMITIC ACID(Covalent)
PLM.6: 6 residues within 4Å:- Chain A: L.51, P.54, I.55, L.322, C.323
- Ligands: C8E.13
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.51, A:P.54, A:I.55
PLM.7: 8 residues within 4Å:- Chain A: F.53, F.57, L.58, Y.61, T.321, L.322, C.323, C.324
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:F.53, A:L.58, A:Y.61, A:L.322
PLM.18: 4 residues within 4Å:- Chain B: P.54, I.55, L.322, C.323
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:P.54, B:I.55, B:L.322
PLM.19: 6 residues within 4Å:- Chain B: F.53, F.57, T.321, L.322, C.323, C.324
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:F.53, B:F.53, B:F.57
- 2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)
PEF.8: 7 residues within 4Å:- Chain A: I.257, A.261, I.264, T.298, Y.302, V.305, I.306
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:I.257, A:A.261, A:I.264, A:Y.302, A:V.305, A:I.306
PEF.22: 5 residues within 4Å:- Chain B: A.261, T.298, Y.302, I.306, M.310
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.261, B:Y.302, B:I.306
- 3 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.9: 8 residues within 4Å:- Chain A: F.213, L.267, G.271, V.272, F.274, Y.275, F.288
- Ligands: C8E.14
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.213, A:F.274
LDA.23: 7 residues within 4Å:- Chain B: F.209, F.213, L.267, G.271, V.272, F.274
- Ligands: LDA.28
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.209, B:F.213, B:F.274, B:F.274
LDA.28: 8 residues within 4Å:- Chain B: L.267, P.268, G.271, V.272, Y.275, F.288
- Ligands: C8E.20, LDA.23
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.267, B:P.268
- 12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)
C8E.10: 6 residues within 4Å:- Chain A: L.41, Y.44, P.268, I.291, P.292, F.295
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.41, A:Y.44, A:P.268
C8E.11: 4 residues within 4Å:- Chain A: T.109, N.112, F.116, L.173
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:N.112, A:F.116, A:L.173
- Hydrogen bonds: A:N.112
C8E.12: 5 residues within 4Å:- Chain A: F.221, Y.224, I.260
- Chain B: T.278
- Ligands: C8E.20
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:F.221
C8E.13: 6 residues within 4Å:- Chain A: I.308, M.309, R.315, N.316, M.318
- Ligands: PLM.6
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:I.308
- Hydrogen bonds: A:R.315
C8E.14: 4 residues within 4Å:- Chain A: F.274, Y.275
- Chain B: L.263
- Ligands: LDA.9
No protein-ligand interaction detected (PLIP)C8E.15: 2 residues within 4Å:- Chain A: F.222
- Chain B: V.210
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.210
C8E.20: 8 residues within 4Å:- Chain A: I.260, L.263
- Chain B: F.274, Y.275, T.278, H.279
- Ligands: C8E.12, LDA.28
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:I.260
- Hydrogen bonds: B:F.274, B:T.278
C8E.21: 3 residues within 4Å:- Chain A: Y.207
- Chain B: I.218, F.222
No protein-ligand interaction detected (PLIP)C8E.24: 4 residues within 4Å:- Chain B: Y.44, I.291, P.292, F.295
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:I.291
C8E.25: 3 residues within 4Å:- Chain B: T.109, N.112, F.116
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:N.112, B:F.116, B:F.116
- Hydrogen bonds: B:N.112
C8E.26: 3 residues within 4Å:- Chain A: T.278
- Chain B: Y.224, I.260
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:T.278, B:Y.224
C8E.27: 4 residues within 4Å:- Chain B: I.308, R.315, N.316, M.318
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:I.308
- Hydrogen bonds: B:R.315
- 2 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, J. et al., Structure of Bovine Rhodopsin in a Trigonal Crystal Form. J.Mol.Biol. (2004)
- Release Date
- 2003-11-20
- Peptides
- RHODOPSIN: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x RET: RETINAL(Covalent)
- 4 x PLM: PALMITIC ACID(Covalent)
- 2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)
- 3 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)
- 2 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, J. et al., Structure of Bovine Rhodopsin in a Trigonal Crystal Form. J.Mol.Biol. (2004)
- Release Date
- 2003-11-20
- Peptides
- RHODOPSIN: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.