SMTL ID : 6nwe.1

Crystal structure of bovine opsin with beta octyl glucoside bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 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: 5 residues within 4Å: Chain A: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)(Post Translational Modification)

BOG.2: 6 residues within 4Å: Chain A: F.220, G.224, K.231, E.247, T.251, V.254 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.220 Hydrogen bonds: A:K.231 Salt bridges: A:K.231 BOG.3: 4 residues within 4Å: Chain A: S.144, F.146, N.151, H.152 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.146 Hydrogen bonds: A:H.152 BOG.4: 3 residues within 4Å: Chain A: Y.96, L.99, H.100 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.96, A:L.99 BOG.5: 4 residues within 4Å: Chain A: Y.136, P.142, F.221, Q.225 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.221, A:F.221 BOG.9: 15 residues within 4Å: Chain A: G.114, T.118, G.121, E.122, E.181, C.187, G.188, I.189, Y.191, M.207, F.212, W.265, Y.268, A.269, A.272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.191, A:M.207, A:F.212, A:Y.268, A:A.272 Hydrogen bonds: A:G.121, A:E.122, A:C.187, A:I.189

1 x PLM: PALMITIC ACID(Covalent)

PLM.6: 3 residues within 4Å: Chain A: L.321, C.322, C.323 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: G.284, P.285, I.286, F.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.284, A:I.286, A:F.287 SO4.8: 4 residues within 4Å: Chain A: E.239, S.240, A.241, T.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.241, A:T.242, A:T.242 SO4.10: 3 residues within 4Å: Chain B: I.1, L.2, E.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.1, B:I.1, B:L.2, B:E.3

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

2020-02-12

Peptides

Rhodopsin: A
ILENLKDVGLF 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 peptide CT2

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