SMTL ID : 6fkd.1

Crystal structure of N2C/D282C stabilized opsin bound to RS16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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 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)

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

BOG.3: 16 residues within 4Å: Chain A: A.118, T.119, G.122, L.129, E.182, G.189, I.190, F.262, C.265, Y.269, A.293, A.296, K.297, S.299, N.303 Ligands: DL2.8 9 PLIP interactions: 9 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.193, A:Y.269, A:Y.269, A:K.297 BOG.4: 13 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, F.294, F.295, K.297 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.287, 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:T.290, A:T.290, A:K.297 BOG.5: 4 residues within 4Å: Chain A: Y.30, Y.97, L.100, H.101 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.97, A:Y.97, A:L.100 Hydrogen bonds: A:H.101 Salt bridges: A:H.101 BOG.6: 8 residues within 4Å: Chain A: F.221, Y.224, G.225, K.232, T.252, V.255, I.256, V.259 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.221, A:Y.224, A:T.252, A:V.255, A:I.256, A:V.259 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.7: 2 residues within 4Å: Chain A: E.34, W.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.34

1 x DL2: 5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one(Non-covalent)

DL2.8: 15 residues within 4Å: Chain A: E.123, L.126, Y.192, V.205, M.208, F.209, H.212, F.213, F.262, C.265, W.266, Y.269, A.273, M.289 Ligands: BOG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.192, A:V.205, A:F.209, A:F.213, A:Y.269, A:Y.269, A:A.273 pi-Stacking: A:F.213

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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