- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x RET: RETINAL(Covalent)4 x PLM: PALMITIC ACID(Covalent)
PLM.2: 6 residues within 4Å:- Chain A: L.51, P.54, I.55, L.322, C.323
- Ligands: C8E.15
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.51, A:P.54, A:I.55
PLM.3: 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.20: 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.21: 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
8 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)(Non-covalent)(Non-functional Binders)NAG.4: 5 residues within 4Å:- Chain A: T.5, N.16, G.19, V.21
- Ligands: NAG.5
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:V.21
NAG.5: 3 residues within 4Å:- Chain A: R.22
- Ligands: NAG.4, BMA.6
No protein-ligand interaction detected (PLIP)NAG.7: 5 residues within 4Å:- Chain A: X.1, N.3, G.281, D.283
- Ligands: NAG.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.281, A:D.283, A:D.283
NAG.8: 2 residues within 4Å:- Ligands: NAG.7, BMA.9
No protein-ligand interaction detected (PLIP)NAG.22: 5 residues within 4Å:- Chain B: T.5, N.16, G.19, V.21
- Ligands: NAG.23
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.16, B:V.21, B:R.22
NAG.23: 2 residues within 4Å:- Ligands: NAG.22, BMA.24
No protein-ligand interaction detected (PLIP)NAG.25: 6 residues within 4Å:- Chain B: X.1, M.2, N.3, G.281, D.283
- Ligands: NAG.26
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.283, B:D.283
NAG.26: 2 residues within 4Å:- Ligands: NAG.25, BMA.27
No protein-ligand interaction detected (PLIP)4 x BMA: BETA-D-MANNOSE(Non-functional Binders)BMA.6: 1 residues within 4Å:- Ligands: NAG.5
No protein-ligand interaction detected (PLIP)BMA.9: 1 residues within 4Å:- Ligands: NAG.8
No protein-ligand interaction detected (PLIP)BMA.24: 1 residues within 4Å:- Ligands: NAG.23
No protein-ligand interaction detected (PLIP)BMA.27: 1 residues within 4Å:- Ligands: NAG.26
No protein-ligand interaction detected (PLIP)2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)PEF.10: 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.30: 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.11: 8 residues within 4Å:- Chain A: F.213, L.267, G.271, V.272, F.274, Y.275, F.288
- Ligands: C8E.16
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.213, A:F.274
LDA.31: 7 residues within 4Å:- Chain B: F.209, F.213, L.267, G.271, V.272, F.274
- Ligands: LDA.36
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.209, B:F.213, B:F.274, B:F.274
LDA.36: 8 residues within 4Å:- Chain B: L.267, P.268, G.271, V.272, Y.275, F.288
- Ligands: C8E.28, LDA.31
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.12: 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.13: 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.14: 5 residues within 4Å:- Chain A: F.221, Y.224, I.260
- Chain B: T.278
- Ligands: C8E.28
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:F.221
C8E.15: 6 residues within 4Å:- Chain A: I.308, M.309, R.315, N.316, M.318
- Ligands: PLM.2
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:I.308
- Hydrogen bonds: A:R.315
C8E.16: 4 residues within 4Å:- Chain A: F.274, Y.275
- Chain B: L.263
- Ligands: LDA.11
No protein-ligand interaction detected (PLIP)C8E.17: 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.28: 8 residues within 4Å:- Chain A: I.260, L.263
- Chain B: F.274, Y.275, T.278, H.279
- Ligands: C8E.14, LDA.36
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.29: 3 residues within 4Å:- Chain A: Y.207
- Chain B: I.218, F.222
No protein-ligand interaction detected (PLIP)C8E.32: 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.33: 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.34: 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.35: 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
- Links
- RCSB PDBe 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- Links
- RCSB PDBe 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