SMTL ID : 6fkb.1

Crystal structure of N2C/D282C stabilized opsin bound to RS13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

monomer

Ligands

1 x PLM: PALMITIC ACID(Covalent)

PLM.1: 3 residues within 4Å: Chain A: V.319, L.322, C.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.323

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 8 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21, R.22, S.23 Ligands: NAG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.5, A:F.10, A:V.21 Hydrogen bonds: A:N.16, A:V.21 NAG.3: 3 residues within 4Å: Chain A: R.22 Ligands: NAG.2, BMA.4 No protein-ligand interaction detected (PLIP)

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.4: 3 residues within 4Å: Ligands: NAG.3, MAN.5, MAN.6 No protein-ligand interaction detected (PLIP)

2 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.5: 1 residues within 4Å: Ligands: BMA.4 No protein-ligand interaction detected (PLIP) MAN.6: 1 residues within 4Å: Ligands: BMA.4 No protein-ligand interaction detected (PLIP)

5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

BOG.7: 4 residues within 4Å: Chain A: Y.97, L.100, H.101 Ligands: BOG.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.97 Hydrogen bonds: A:H.101 Salt bridges: A:H.101 BOG.8: 15 residues within 4Å: Chain A: A.118, T.119, G.122, L.126, L.129, E.182, G.189, I.190, C.265, Y.269, A.293, K.297, S.299, N.303 Ligands: DLH.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.126, A:L.129 Hydrogen bonds: A:E.182, A:I.190, A:Y.269, A:Y.269 BOG.9: 11 residues within 4Å: Chain A: L.41, E.182, M.184, Q.185, C.186, S.187, I.287, T.290, A.293, F.294, K.297 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.287, A:I.287, A:F.294, A:F.294, A:F.294 Hydrogen bonds: A:E.182, A:M.184, A:C.186, A:C.186, A:S.187, A:S.187, A:T.290, A:T.290, A:K.297, A:K.297 BOG.10: 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:Y.224, A:T.252, A:V.255, A:I.256, A:I.256, A:V.259 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.11: 1 residues within 4Å: Ligands: BOG.7 No protein-ligand interaction detected (PLIP)

1 x DLH: 2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone(Non-covalent)

DLH.12: 12 residues within 4Å: Chain A: E.123, L.126, Y.192, V.205, M.208, H.212, F.213, C.265, W.266, Y.269, A.273 Ligands: BOG.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.126, A:L.126, A:Y.192, A:V.205, 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