SMTL ID : 6ph7.2 (1 other biounit)

Crystal structure of bovine opsin with nerol bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 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-BMA.5: 5 residues within 4Å: Chain C: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

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

BOG.2: 4 residues within 4Å: Chain A: Y.96, L.99, H.100 Chain C: W.35 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.96, A:Y.96, A:L.99, C:W.35 Hydrogen bonds: A:H.100 Salt bridges: A:H.100 BOG.6: 4 residues within 4Å: Chain A: W.35 Chain C: Y.96, L.99, H.100 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:W.35, C:Y.96, C:Y.96, C:L.99 Hydrogen bonds: C:H.100 Salt bridges: C:H.100

2 x PLM: PALMITIC ACID(Covalent)

PLM.3: 10 residues within 4Å: Chain A: L.321, C.322, C.323 Chain C: L.46, R.252, I.256, T.297, Y.301, V.304, M.309 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.46, C:I.256, C:V.304 PLM.7: 10 residues within 4Å: Chain A: L.46, R.252, I.256, T.297, Y.301, V.304, M.309 Chain C: L.321, C.322, C.323 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.46, A:I.256, A:V.304

2 x NZZ: (2Z)-3,7-dimethylocta-2,6-dien-1-ol(Non-covalent)

NZZ.4: 11 residues within 4Å: Chain A: E.122, Y.191, V.204, M.207, F.208, H.211, F.212, W.265, Y.268, A.269, A.272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.191, A:V.204, A:F.208, A:F.212, A:F.212, A:Y.268, A:A.269, A:A.272 Hydrogen bonds: A:E.122 NZZ.8: 11 residues within 4Å: Chain C: E.122, Y.191, V.204, M.207, F.208, H.211, F.212, W.265, Y.268, A.269, A.272 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.191, C:V.204, C:F.208, C:F.212, C:F.212, C:Y.268, C:A.269, C:A.272 Hydrogen bonds: C: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: AC
G protein CT2 peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

G protein CT2 peptide

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