SMTL ID : 3c9l.1

Structure of ground-state bovine rhodospin in a hexagonal crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

2 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

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.2, G.280, D.282 Ligands: ACE.4 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: R.147, G.149, E.150, N.151, H.152 No protein-ligand interaction detected (PLIP)

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

ACE.4: 3 residues within 4Å: Chain A: M.1, N.2 Ligands: NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP)

1 x RET: RETINAL(Covalent)

RET.5: 16 residues within 4Å: Chain A: E.113, A.117, T.118, G.121, E.122, C.187, G.188, I.189, Y.191, M.207, F.212, F.261, W.265, Y.268, A.292, K.296 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.117, A:T.118, A:I.189, A:F.212, A:F.261, A:W.265, A:Y.268, A:Y.268, A:K.296

2 x PLM: PALMITIC ACID(Covalent)

PLM.6: 6 residues within 4Å: Chain A: L.50, P.53, I.54, L.321, C.322 Ligands: C8E.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.50, A:P.53, A:I.54 PLM.7: 8 residues within 4Å: Chain A: F.52, F.56, L.57, Y.60, T.320, L.321, C.322, C.323 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.52, A:F.52, A:L.57, A:Y.60, A:L.321

1 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.8: 7 residues within 4Å: Chain A: I.256, A.260, I.263, T.297, Y.301, V.304, I.305 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.256, A:A.260, A:I.263, A:Y.301, A:V.304, A:I.305

1 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.9: 7 residues within 4Å: Chain A: F.212, L.266, G.270, V.271, F.273, Y.274 Ligands: C8E.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.212, A:F.273, A:F.273

6 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.10: 6 residues within 4Å: Chain A: L.40, Y.43, P.267, I.290, P.291, F.294 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.40, A:Y.43, A:P.267 C8E.11: 4 residues within 4Å: Chain A: T.108, N.111, F.115, L.172 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.111, A:F.115, A:F.115, A:L.172 Hydrogen bonds: A:N.111 C8E.12: 3 residues within 4Å: Chain A: F.220, Y.223, I.259 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.220 C8E.13: 6 residues within 4Å: Chain A: I.307, M.308, R.314, N.315, M.317 Ligands: PLM.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.307 Hydrogen bonds: A:R.314 C8E.14: 3 residues within 4Å: Chain A: F.273, Y.274 Ligands: LDA.9 No protein-ligand interaction detected (PLIP) C8E.15: 1 residues within 4Å: Chain A: F.221 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stenkamp, R.E., Alternative models for two crystal structures of bovine rhodopsin. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-08-05

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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