SMTL ID : 6fk9.1

Crystal structure of N2C/D282C stabilized opsin bound to RS09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 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: 5 residues within 4Å: Chain A: T.5, N.16, G.19, V.21, R.22 No protein-ligand interaction detected (PLIP)

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)

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

BOG.3: 17 residues within 4Å: Chain A: A.118, T.119, G.122, L.129, E.182, C.188, G.189, I.190, Y.192, C.265, Y.269, A.293, A.296, K.297, S.299, N.303 Ligands: DNK.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.129, A:A.296 Hydrogen bonds: A:E.182, A:C.188, A:I.190, A:Y.192, A:Y.192, A:K.297 Salt bridges: A:K.297 BOG.4: 14 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, K.297 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.287, A:I.287, A:I.291, A:F.294, A:F.294, A:F.294 Hydrogen bonds: A:E.182, A:M.184, A:Q.185, A:C.186, A:S.187, A:T.290, A:T.290, A:K.297 BOG.5: 8 residues within 4Å: Chain A: F.221, Y.224, G.225, K.232, T.252, V.255, I.256, V.259 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.221, A:V.255, A:I.256, A:I.256, A:V.259 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.6: 4 residues within 4Å: Chain A: Y.30, Y.97, L.100, H.101 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.97, A:Y.97, A:L.100 Hydrogen bonds: A:Y.30, A:H.101 Salt bridges: A:H.101

1 x DNK: (2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one(Non-covalent)

DNK.7: 12 residues within 4Å: Chain A: G.122, E.123, L.126, Y.192, M.208, F.209, H.212, F.213, C.265, Y.269, A.273 Ligands: BOG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.123, A:L.126, A:Y.192, A:M.208, A:F.209, A:F.209, A:F.213, A:Y.269, A:A.273 pi-Stacking: A:F.213, A:F.213, A:Y.269

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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