SMTL ID : 2ziy.2 (1 other biounit)

Crystal structure of squid rhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 13 residues within 4Å: Chain A: N.86, Y.110, G.115, F.119, N.184, C.185, S.186, M.203, F.204, F.208, W.273, A.277, K.304 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.110, A:F.119, A:F.119, A:F.204, A:F.208, A:W.273, A:W.273, A:W.273, A:A.277, A:K.304 RET.4: 13 residues within 4Å: Chain B: N.86, Y.110, G.115, F.119, N.184, C.185, S.186, M.203, F.204, F.208, W.273, A.277, K.304 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.110, B:F.119, B:F.119, B:F.204, B:F.208, B:W.273, B:W.273, B:W.273, B:A.277, B:K.304

4 x PLM: PALMITIC ACID(Covalent)

PLM.2: 2 residues within 4Å: Chain A: C.335 Ligands: PLM.3 No protein-ligand interaction detected (PLIP) PLM.3: 6 residues within 4Å: Chain A: S.315, V.316, V.332, C.335, C.336 Ligands: PLM.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.316 Hydrogen bonds: A:C.335 PLM.5: 2 residues within 4Å: Chain B: C.335 Ligands: PLM.6 No protein-ligand interaction detected (PLIP) PLM.6: 6 residues within 4Å: Chain B: S.315, V.316, V.332, C.335, C.336 Ligands: PLM.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.316 Hydrogen bonds: B:C.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimamura, T. et al., Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J.Biol.Chem. (2008)

Release Date

2008-05-06

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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