SMTL ID : 3aym.1 (1 other biounit)

Crystal structure of the batho intermediate of squid rhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 4 residues within 4Å: Chain A: I.56, K.61, F.78, F.81 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.56, A:F.78, A:F.81 Hydrogen bonds: A:K.61

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

BOG.2: 15 residues within 4Å: Chain A: T.67, A.69, N.70, I.73, I.129, D.132, R.133, K.146, E.256, L.259, I.262, S.263, K.321, D.347, E.351 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.69, A:I.129, A:I.262 Hydrogen bonds: A:K.321, A:D.347, A:E.351 Salt bridges: A:R.133

1 x RET: RETINAL(Covalent)

RET.3: 18 residues within 4Å: Chain A: G.115, G.116, G.119, F.120, I.123, E.180, N.185, C.186, S.187, F.188, M.204, F.205, F.209, F.270, W.274, A.278, V.301, K.305 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.120, A:F.120, A:I.123, A:F.188, A:F.205, A:F.209, A:F.209, A:F.209, A:F.209, A:F.270, A:F.270, A:W.274, A:W.274, A:A.278, A:V.301, A:K.305, A:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M. et al., Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin. J.Mol.Biol. (2011)

Release Date

2011-08-17

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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