- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x ACE: ACETYL GROUP(Non-functional Binders)
- 2 x RET: RETINAL(Covalent)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 7 residues within 4Å:- Chain A: M.1, N.2, Q.279, G.280, S.281, D.282
- Ligands: ACE.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.282
NAG.20: 6 residues within 4Å:- Chain B: M.1, N.2, G.280, S.281, D.282
- Ligands: ACE.18
1 PLIP interactions:1 interactions with chain B- Water bridges: B:D.282
- 1 x DAO: LAURIC ACID(Non-covalent)
- 13 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
OLC.7: 7 residues within 4Å:- Chain A: I.263, G.270, V.271, Y.274, D.282, F.283, F.287
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:I.263, A:V.271, A:Y.274, A:F.287
- Hydrogen bonds: A:D.282
- Water bridges: A:Y.274
OLC.8: 10 residues within 4Å:- Chain A: R.69, Y.74, L.77, N.78, V.81, V.157, W.161
- Chain B: Y.274, H.278
- Ligands: OLC.14
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.74, A:L.77, A:V.81, A:V.157
- Hydrogen bonds: A:R.69
- Salt bridges: A:R.69
OLC.9: 2 residues within 4Å:- Chain A: I.213, F.273
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.273, A:F.273, A:F.273
OLC.10: 4 residues within 4Å:- Chain A: Q.36, L.40, I.290, F.294
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.40, A:I.290
OLC.11: 1 residues within 4Å:- Chain A: M.308
No protein-ligand interaction detected (PLIP)OLC.13: 2 residues within 4Å:- Chain A: Y.223, V.227
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.227
OLC.14: 12 residues within 4Å:- Chain A: Y.74, E.150, N.151, W.161, L.165
- Chain B: G.270, V.271, Y.274, D.282, F.283, F.287
- Ligands: OLC.8
12 PLIP interactions:5 interactions with chain A, 7 interactions with chain B- Hydrophobic interactions: A:W.161, A:L.165, B:V.271, B:Y.274, B:Y.274, B:Y.274, B:F.287
- Hydrogen bonds: A:Y.74, A:N.151, B:D.282
- Water bridges: A:N.151, B:D.282
OLC.15: 5 residues within 4Å:- Chain A: N.111, L.112, F.115, L.172
- Chain B: Y.223
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:N.111, A:L.112, A:F.115, A:L.172
- Hydrogen bonds: A:N.111
OLC.16: 7 residues within 4Å:- Chain A: H.152
- Chain B: W.35, Q.36, L.40, Y.43, F.293, F.294
6 PLIP interactions:1 interactions with chain A, 5 interactions with chain B- Salt bridges: A:H.152
- Hydrophobic interactions: B:W.35, B:L.40, B:Y.43, B:F.293, B:F.294
OLC.17: 4 residues within 4Å:- Chain A: P.170, V.173
- Chain B: I.263, M.308
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:P.170, A:V.173, B:I.263
OLC.21: 6 residues within 4Å:- Chain B: V.63, K.66, R.69, Y.74, N.78, W.161
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:Y.74, B:W.161
- Salt bridges: B:K.66, B:R.69
OLC.22: 10 residues within 4Å:- Chain A: N.151, I.154, A.158, F.159
- Chain B: P.267, V.271, I.286, F.287, I.290, P.291
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:P.267, B:I.290, A:A.158, A:F.159
- Hydrogen bonds: B:I.286, A:N.151
OLC.24: 4 residues within 4Å:- Chain B: F.208, F.212, I.213, F.273
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.208, B:F.212, B:I.213, B:F.273
- 2 x PLM: PALMITIC ACID(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gruhl, T. et al., Ultrafast structural changes direct the first molecular events of vision. Nature (2023)
- Release Date
- 2023-03-29
- 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 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x ACE: ACETYL GROUP(Non-functional Binders)
- 2 x RET: RETINAL(Covalent)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x DAO: LAURIC ACID(Non-covalent)
- 13 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 2 x PLM: PALMITIC ACID(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gruhl, T. et al., Ultrafast structural changes direct the first molecular events of vision. Nature (2023)
- Release Date
- 2023-03-29
- Peptides
- Rhodopsin: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.