SMTL ID : 8a6e.1

100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)

Coordinates

PDB Format Compare

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)

NAG-NAG.1: 5 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain B: T.5, F.10, N.16, G.19, V.21 No protein-ligand interaction detected (PLIP)

2 x RET: RETINAL(Covalent)

RET.2: 16 residues within 4Å: Chain A: E.114, A.118, T.119, G.122, E.123, S.187, C.188, Y.192, M.208, H.212, F.213, F.262, W.266, Y.269, A.293, K.297 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.119, A:E.123, A:F.213, A:F.213, A:F.262, A:W.266, A:Y.269, A:Y.269, A:A.293, A:K.297 RET.17: 16 residues within 4Å: Chain B: E.114, A.118, T.119, G.122, E.123, S.187, C.188, Y.192, M.208, F.213, F.262, W.266, Y.269, A.270, A.293, K.297 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.123, B:F.213, B:F.262, B:W.266, B:Y.269, B:Y.269, B:A.270, B:A.293, B:K.297

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 7 residues within 4Å: Chain A: X.1, M.2, N.3, Q.280, G.281, S.282, D.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.283 NAG.18: 7 residues within 4Å: Chain B: X.1, M.2, N.3, Q.280, G.281, S.282, D.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.3 Water bridges: B:D.283

1 x DAO: LAURIC ACID(Non-covalent)

DAO.4: 6 residues within 4Å: Chain A: P.268, V.272, I.287, F.288, P.292, F.295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.268, A:P.292, A:F.295

13 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 8 residues within 4Å: Chain A: I.264, L.267, G.271, V.272, Y.275, D.283, F.284, F.288 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.264, A:L.267, A:Y.275, A:F.288 Hydrogen bonds: A:D.283 Water bridges: A:Y.275 OLC.6: 8 residues within 4Å: Chain A: R.70, Y.75, L.78, N.79, V.82, V.158, W.162 Ligands: OLC.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.75, A:L.78, A:V.82, A:V.158, A:W.162 Hydrogen bonds: A:R.70 Salt bridges: A:R.70 OLC.7: 4 residues within 4Å: Chain A: F.209, F.213, I.214, F.274 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.209, A:F.213, A:F.274, A:F.274, A:F.274 OLC.8: 6 residues within 4Å: Chain A: Q.37, M.40, L.41, I.287, I.291, F.295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.287, A:I.291, A:F.295 OLC.9: 1 residues within 4Å: Chain A: M.309 No protein-ligand interaction detected (PLIP) OLC.11: 2 residues within 4Å: Chain A: Y.224, V.228 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.224, A:V.228 OLC.12: 8 residues within 4Å: Chain A: Y.75, E.151, N.152, I.155, A.159, W.162, L.166 Ligands: OLC.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.155, A:I.155, A:A.159, A:W.162, A:L.166 Hydrogen bonds: A:Y.75, A:N.152 Water bridges: A:N.152 OLC.13: 4 residues within 4Å: Chain A: N.112, L.113, F.116, L.173 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.113, A:F.116, A:L.173, A:L.173 Hydrogen bonds: A:N.112 OLC.14: 1 residues within 4Å: Chain A: H.153 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.153 OLC.15: 1 residues within 4Å: Chain A: V.174 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.174 OLC.19: 4 residues within 4Å: Chain B: V.64, R.70, Y.75, W.162 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.75 Salt bridges: B:R.70 OLC.20: 5 residues within 4Å: Chain B: P.268, I.287, F.288, I.291, P.292 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.291, B:P.292 Hydrogen bonds: B:I.287 OLC.22: 4 residues within 4Å: Chain B: F.213, I.214, G.271, F.274 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.213, B:I.214, B:F.274

2 x PLM: PALMITIC ACID(Covalent)

PLM.10: 8 residues within 4Å: Chain A: L.322, C.323 Chain B: M.50, L.51, R.315, M.318, V.319, L.322 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.51, B:V.319, B:L.322 PLM.21: 5 residues within 4Å: Chain A: R.315, M.318, V.319 Chain B: L.322, C.323 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.322, A:V.319

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
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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