SMTL ID : 6fk7.1

Crystal structure of N2C/D282C stabilized opsin bound to RS06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

2 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 NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain B: T.5, F.10, N.16, G.19, V.21, R.22 No protein-ligand interaction detected (PLIP)

2 x PLM: PALMITIC ACID(Covalent)

PLM.2: 8 residues within 4Å: Chain A: V.319, L.322, C.323 Chain B: I.257, T.298, V.301, Y.302, M.310 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.257, B:T.298, B:Y.302 PLM.10: 8 residues within 4Å: Chain A: I.257, T.298, V.301, Y.302, M.310 Chain B: V.319, L.322, C.323 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.257, A:T.298, A:Y.302

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

BOG.3: 14 residues within 4Å: Chain A: A.118, G.122, L.129, E.182, G.189, I.190, F.262, C.265, Y.269, A.293, A.296, S.299, N.303 Ligands: DO5.8 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: 11 residues within 4Å: Chain A: E.182, G.183, M.184, Q.185, C.186, S.187, P.286, I.287, T.290, F.294, K.297 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.287, A:F.294 Hydrogen bonds: A:E.182, A:M.184, A:C.186, A:S.187, A:S.187, A:T.290, A:T.290, A:K.297, A:K.297 BOG.5: 6 residues within 4Å: Chain A: Y.97, L.100, H.101 Chain B: E.34, W.36 Ligands: BOG.7 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.97, A:L.100, B:W.36, B:W.36, B:W.36 Hydrogen bonds: A:Y.30, A:H.101 Salt bridges: A:H.101 BOG.6: 7 residues within 4Å: Chain A: F.221, Y.224, G.225, K.232, T.252, I.256, V.259 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.221, A:Y.224, A:I.256, A:V.259 Salt bridges: A:K.232 BOG.7: 3 residues within 4Å: Chain A: Y.97 Chain B: W.36 Ligands: BOG.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.34 BOG.11: 14 residues within 4Å: Chain B: A.118, G.122, L.129, E.182, G.189, I.190, F.262, C.265, Y.269, A.293, A.296, S.299, N.303 Ligands: DO5.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.129, B:F.262, B:A.296 Hydrogen bonds: B:E.182, B:I.190, B:Y.193, B:Y.269, B:K.297 BOG.12: 11 residues within 4Å: Chain B: E.182, G.183, M.184, Q.185, C.186, S.187, P.286, I.287, T.290, F.294, K.297 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.287, B:F.294 Hydrogen bonds: B:M.184, B:C.186, B:S.187, B:S.187, B:T.290, B:T.290, B:K.297, B:K.297 BOG.13: 6 residues within 4Å: Chain A: E.34, W.36 Chain B: Y.97, L.100, H.101 Ligands: BOG.15 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.97, B:L.100, A:W.36, A:W.36, A:W.36 Hydrogen bonds: B:H.101, A:E.34 Salt bridges: B:H.101 BOG.14: 7 residues within 4Å: Chain B: F.221, Y.224, G.225, K.232, T.252, I.256, V.259 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.221, B:Y.224, B:I.256, B:V.259 Salt bridges: B:K.232 BOG.15: 3 residues within 4Å: Chain A: W.36 Chain B: Y.97 Ligands: BOG.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.34, B:Y.97

2 x DO5: (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one(Non-covalent)

DO5.8: 15 residues within 4Å: Chain A: 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, M.289 Ligands: BOG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.126, A:V.205, A:F.209, A:F.209, A:Y.269, A:A.273 Hydrogen bonds: A:E.123 pi-Stacking: A:F.213, A:Y.269 DO5.16: 15 residues within 4Å: Chain B: 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, M.289 Ligands: BOG.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.126, B:V.205, B:F.209, B:F.209, B:Y.269, B:A.273 pi-Stacking: B:F.213, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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