SMTL ID : 6fkc.1

Crystal structure of N2C/D282C stabilized opsin bound to RS15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 6 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21, R.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.2

1 x PLM: PALMITIC ACID(Covalent)

PLM.2: 3 residues within 4Å: Chain A: V.319, L.322, C.323 No protein-ligand interaction detected (PLIP)

1 x DLB: 3-[1'-[(2~{S})-2-(4-chlorophenyl)-3-methyl-butanoyl]spiro[1,3-benzodioxole-2,4'-piperidine]-5-yl]propanoic acid(Non-covalent)

DLB.3: 17 residues within 4Å: Chain A: T.119, G.122, E.123, L.126, Y.192, V.205, M.208, F.209, H.212, F.213, C.265, W.266, Y.269, A.273, I.276, M.289 Ligands: BOG.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.119, A:E.123, A:L.126, A:F.209, A:F.213, A:F.213, A:Y.269, A:Y.269, A:A.273, A:I.276 pi-Stacking: A:Y.192

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

BOG.4: 3 residues within 4Å: Chain A: Y.30, L.100, H.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.100 Hydrogen bonds: A:H.101 Salt bridges: A:H.101 BOG.5: 15 residues within 4Å: Chain A: A.118, T.119, G.122, L.129, E.182, G.189, F.262, C.265, Y.269, A.293, A.296, K.297, S.299, N.303 Ligands: DLB.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.129, A:F.262, A:A.296 Hydrogen bonds: A:E.182, A:I.190, A:Y.269, A:K.297 BOG.6: 4 residues within 4Å: Chain A: F.221, G.225, K.232, V.259 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.259 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.7: 15 residues within 4Å: Chain A: L.41, E.182, G.183, M.184, Q.185, C.186, S.187, P.286, I.287, T.290, I.291, A.293, F.294, F.295, K.297 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.291, A:F.294, A:F.294, A:F.294, A:F.294, A:F.295 Hydrogen bonds: A:E.182, A:M.184, A:Q.185, A:C.186, A:S.187, A:S.187, A:T.290, A:T.290, A:K.297, A:K.297 BOG.8: 2 residues within 4Å: Chain A: E.34, W.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattle, D. et al., Ligand channel in pharmacologically stabilized rhodopsin. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-04

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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