SMTL ID : 2z73.1 (3 other biounits)

Crystal structure of squid rhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

BOG.1: 14 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, S.263, K.321, D.347, E.351 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.69, A:I.129 Hydrogen bonds: A:K.321, A:D.347, A:E.351 Salt bridges: A:K.146

1 x RET: RETINAL(Covalent)

RET.2: 18 residues within 4Å: Chain A: N.87, Y.111, G.112, G.115, G.116, G.119, F.120, N.185, C.186, S.187, F.188, M.204, F.205, F.209, W.274, A.278, V.301, K.305 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.111, A:F.120, A:F.120, A:F.188, A:F.188, A:F.188, A:F.205, A:F.205, A:F.205, A:F.209, A:F.209, A:W.274, A:W.274, A:A.278, A:V.301, A:K.305

2 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.3: 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 PLM.4: 7 residues within 4Å: Chain A: I.47, M.313, S.316, V.317, V.333, C.337 Ligands: TWT.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.47

1 x TWT: DOCOSANE(Non-covalent)

TWT.5: 6 residues within 4Å: Chain A: I.47, G.50, G.51, P.312, V.333 Ligands: PLM.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.47, A:P.312, A:V.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M. et al., Crystal structure of squid rhodopsin. Nature (2008)

Release Date

2008-05-13

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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