SMTL ID : 2i35.1

Crystal structure of rhombohedral crystal form of ground-state rhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: T.5, N.16, G.19, V.21, R.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.22

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: X.1, N.3, D.283 No protein-ligand interaction detected (PLIP)

1 x RET: RETINAL(Non-covalent)

RET.3: 12 residues within 4Å: Chain A: A.118, T.119, G.122, C.188, Y.192, M.208, F.213, F.262, W.266, Y.269, A.293, K.297 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.118, A:T.119, A:F.213, A:F.213, A:F.262, A:W.266, A:W.266, A:Y.269, A:Y.269, A:A.293, A:K.297

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 5 residues within 4Å: Chain A: M.50, L.51, P.54, I.55 Ligands: PLM.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.51, A:P.54, A:P.54, A:I.55 PLM.5: 8 residues within 4Å: Chain A: F.53, P.54, L.58, T.321, L.322, C.323, C.324 Ligands: PLM.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.53, A:P.54, A:L.58, A:L.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salom, D. et al., Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-10-17

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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