SMTL ID : 6pel.1

Crystal structure of bovine opsin with citronellol bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 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: 6 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

1 x ODM: (3R)-3,7-dimethyloct-6-en-1-ol(Non-covalent)

ODM.2: 10 residues within 4Å: Chain A: E.122, Y.191, V.204, M.207, H.211, W.265, Y.268, A.269, A.272, F.273 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.191, A:V.204, A:Y.268, A:A.272 Hydrogen bonds: A:E.122

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

BOG.3: 7 residues within 4Å: Chain A: F.220, Y.223, G.224, K.231, T.251, V.254, I.255 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.220, A:T.251, A:V.254, A:I.255, A:I.255 Hydrogen bonds: A:K.231 Salt bridges: A:K.231

1 x PLM: PALMITIC ACID(Covalent)

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

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

2020-06-24

Peptides

Rhodopsin: A
ILENLKDVGLF G alpha peptide CT2: 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

ILENLKDVGLF G alpha peptide CT2

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