SMTL ID : 6i9k.1

Crystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: Y.126, G.127, S.131, S.199, T.201, I.202, Y.218, V.222, Y.223, W.286, W.290, Y.293, L.294, S.297, A.317, K.321 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.126, A:I.202, A:Y.218, A:Y.218, A:V.222, A:Y.223, A:W.286, A:W.290, A:Y.293, A:L.294, A:A.317, A:K.321

11 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 4 residues within 4Å: Chain A: N.210, S.213, F.221 Ligands: OLC.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.221 OLC.3: 4 residues within 4Å: Chain A: Y.234, V.238, F.273, F.280 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.234, A:Y.234, A:V.238, A:F.280, A:F.280 OLC.4: 3 residues within 4Å: Chain A: L.168, F.172, W.176 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.172, A:F.172, A:F.172, A:W.176 OLC.5: 5 residues within 4Å: Chain A: M.45, T.47, I.109, A.113, E.114 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.113 OLC.6: 6 residues within 4Å: Chain A: I.209, S.213, I.216, I.220, F.221 Ligands: OLC.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.209, A:I.216, A:I.220, A:F.221 OLC.7: 5 residues within 4Å: Chain A: L.146, Y.149, N.150, F.228, Y.232 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.146, A:Y.149, A:Y.232, A:Y.232, A:Y.232 OLC.8: 6 residues within 4Å: Chain A: L.294, T.295, F.298, L.299, F.302, S.303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.294, A:F.298, A:L.299, A:F.302 OLC.9: 9 residues within 4Å: Chain A: I.63, S.66, G.67, V.70, V.71, L.74, P.328, I.329, Y.331 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.70, A:V.71, A:L.74, A:P.328, A:I.329, A:Y.331 OLC.10: 5 residues within 4Å: Chain A: F.121, E.124, M.128, M.185, Y.186 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.121, A:M.185 OLC.11: 4 residues within 4Å: Chain A: E.46, M.49, I.52, M.311 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.52 OLC.12: 1 residues within 4Å: Chain A: W.180 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varma, N. et al., Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-07-03

Peptides

Kumopsin1: 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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Kumopsin1