SMTL ID : 4j4q.1

Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-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-MAN.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 GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.2: 4 residues within 4Å: Chain A: K.66, R.69, Y.74, E.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66, A:R.69 Salt bridges: A:R.69

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

BOG.3: 12 residues within 4Å: Chain A: A.117, T.118, C.187, G.188, I.189, Y.191, M.207, F.212, Y.268, A.292, A.295, K.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.191, A:M.207, A:F.212, A:Y.268 Hydrogen bonds: A:T.118, A:I.189 Water bridges: A:K.296 BOG.4: 5 residues within 4Å: Chain A: G.224, K.231, E.247, T.251, V.254 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.231 BOG.5: 5 residues within 4Å: Chain A: P.27, Y.29, 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 BOG.6: 4 residues within 4Å: Chain A: Y.136, P.142, F.221, Q.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.136

1 x PLM: PALMITIC ACID(Covalent)

PLM.7: 3 residues within 4Å: Chain A: L.321, C.322, C.323 No protein-ligand interaction detected (PLIP)

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

SO4.8: 4 residues within 4Å: Chain A: G.284, P.285, I.286, F.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.286, A:F.287 SO4.10: 3 residues within 4Å: Chain B: I.1, L.2, E.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.1, B:I.1, B:L.2, B:E.3, B:E.3, B:E.3 Water bridges: B:N.4

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 6 residues within 4Å: Chain A: V.204, I.205, F.208, A.272, F.273, F.276 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.H. et al., Opsin, a structural model for olfactory receptors?. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2013-10-30

Peptides

Rhodopsin: A
Guanine nucleotide-binding protein G(t) subunit alpha-1: 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

Guanine nucleotide-binding protein G(t) subunit alpha-1

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