SMTL ID : 3aym.2 (1 other biounit)

Crystal structure of the batho intermediate of squid rhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.148, R.150, R.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.148 Salt bridges: A:K.145, A:R.151

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 6 residues within 4Å: Chain A: R.193, S.195, R.198, S.199, L.202, C.203 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.198, A:L.202 Salt bridges: A:R.198, A:R.198

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

BOG.3: 12 residues within 4Å: Chain A: T.67, A.69, N.70, I.73, I.129, R.133, E.256, L.259, I.262, S.263, D.347, E.351 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.69, A:I.73, A:I.129, A:L.259, A:L.259, A:I.262 Hydrogen bonds: A:T.67, A:R.133, A:E.256, A:D.347, A:E.351, A:E.351 Water bridges: A:R.133 Salt bridges: A:K.146

1 x RET: RETINAL(Covalent)

RET.4: 16 residues within 4Å: Chain A: F.83, N.87, G.115, G.116, G.119, F.120, N.185, C.186, S.187, F.188, F.205, F.209, W.274, A.278, V.301, K.305 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.83, A:F.120, A:F.120, A:F.188, 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, 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
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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