SMTL ID : 7zbe.1

Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)

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.4, F.9, N.15, G.18, V.20 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: T.4, F.9, N.15, G.18, V.20 No protein-ligand interaction detected (PLIP)

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.3: 4 residues within 4Å: Chain A: M.1, N.2, G.280 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) ACE.17: 3 residues within 4Å: Chain B: M.1, N.2 Ligands: NAG.19 No protein-ligand interaction detected (PLIP)

2 x RET: RETINAL(Covalent)

RET.4: 15 residues within 4Å: Chain A: E.113, A.117, T.118, G.121, E.122, C.187, I.189, Y.191, M.207, F.212, F.261, W.265, Y.268, A.292, K.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.117, A:I.189, A:F.212, A:F.261, A:W.265, A:Y.268, A:K.296 RET.18: 17 residues within 4Å: Chain B: E.113, A.117, T.118, G.121, E.122, S.186, C.187, I.189, Y.191, M.207, F.212, F.261, W.265, Y.268, A.269, A.292, K.296 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.117, B:I.189, B:F.212, B:F.261, B:W.265, B:Y.268, B:Y.268, B:A.269, B:K.296

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.19: 7 residues within 4Å: Chain B: M.1, N.2, Q.279, G.280, S.281, D.282 Ligands: ACE.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.282

1 x DAO: LAURIC ACID(Non-covalent)

DAO.6: 5 residues within 4Å: Chain A: P.267, I.286, F.287, I.290, P.291 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.267, A:I.290

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

OLC.7: 6 residues within 4Å: Chain A: G.270, V.271, Y.274, D.282, F.283, F.287 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.271, A:Y.274, A:F.287 Hydrogen bonds: A:D.282 Water bridges: A:Y.274 OLC.8: 6 residues within 4Å: Chain A: V.63, Y.74, N.78, V.157, W.161 Ligands: OLC.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.74, A:V.157, A:W.161 Salt bridges: A:R.69 OLC.9: 4 residues within 4Å: Chain A: F.208, I.213, G.270, F.273 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.208, A:I.213, A:F.273, A:F.273 OLC.10: 4 residues within 4Å: Chain A: L.40, Y.43, I.290, F.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.40, A:Y.43, A:I.290, A:F.294 OLC.11: 2 residues within 4Å: Chain A: I.256, M.308 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.256 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: 11 residues within 4Å: Chain A: Y.74, E.150, N.151, W.161, L.165 Chain B: V.271, Y.274, D.282, F.283, F.287 Ligands: OLC.8 11 PLIP interactions: 5 interactions with chain A, 6 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 OLC.15: 4 residues within 4Å: Chain A: N.111, L.112, L.172 Chain B: Y.223 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.111, A:L.112, A:L.172 Hydrogen bonds: A:N.111 OLC.16: 4 residues within 4Å: Chain A: V.173 Chain B: I.256, I.263, M.308 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.256, B:I.263, A:V.173 OLC.20: 6 residues within 4Å: Chain B: V.63, R.69, Y.74, N.78, V.157, W.161 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.74, B:V.157, B:W.161 Salt bridges: B:R.69 OLC.21: 8 residues within 4Å: Chain A: N.151, I.154, A.158 Chain B: P.267, I.286, F.287, I.290, P.291 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.158, B:P.267, B:I.290 Hydrogen bonds: A:N.151, B:I.286 OLC.22: 6 residues within 4Å: Chain B: Q.36, L.40, Y.43, I.286, F.293, F.294 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.40, B:Y.43, B:I.286, B:F.293, B:F.294 OLC.24: 5 residues within 4Å: Chain B: F.208, F.212, I.213, G.270, 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)

PLM.12: 2 residues within 4Å: Chain A: L.321, C.322 No protein-ligand interaction detected (PLIP) PLM.23: 2 residues within 4Å: Chain B: L.321, C.322 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.321

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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