SMTL ID : 6pgs.1

Crystal structure of bovine opsin with geraniol bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.1: 7 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21, S.22 No protein-ligand interaction detected (PLIP)

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 3 residues within 4Å: Chain A: Y.96, L.99, H.100 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.96, A:Y.96, A:L.99 Hydrogen bonds: A:H.100 Salt bridges: A:H.100

1 x PLM: PALMITIC ACID(Covalent)

PLM.3: 3 residues within 4Å: Chain A: L.321, C.322, C.323 No protein-ligand interaction detected (PLIP)

1 x 64Z: Geraniol(Non-covalent)

64Z.4: 10 residues within 4Å: Chain A: E.122, Y.191, M.207, F.208, H.211, F.212, W.265, Y.268, A.269, A.272 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.191, A:M.207, A:F.208, A:F.212, A:F.212, A:Y.268, A:Y.268 Hydrogen bonds: A:E.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morizumi, T. et al., Odorant-binding site in visual opsin. To Be Published

Release Date

2020-07-01

Peptides

Rhodopsin: A
G alpha CT2 peptide: B

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

G alpha CT2 peptide

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