SMTL ID : 1u19.1 (1 other biounit)

Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

NAG-NAG-MAN.1: 4 residues within 4Å: Chain A: T.5, N.16, G.19, V.21 No protein-ligand interaction detected (PLIP)

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: 4 residues within 4Å: Chain A: N.3, G.281, S.282, D.283 No protein-ligand interaction detected (PLIP)

3 x HG: MERCURY (II) ION(Non-covalent)

HG.3: 5 residues within 4Å: Chain A: A.261, C.265, F.295, T.298, Y.302 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.265 HG.4: 4 residues within 4Å: Chain A: A.133, C.223, Y.224, L.227 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.223 HG.5: 4 residues within 4Å: Chain A: Q.313, C.317, T.337, V.338 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.317, H2O.2

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: E.202, Q.280 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.202, A:E.202 ZN.7: 3 residues within 4Å: Chain A: K.312, G.330, D.331 No protein-ligand interaction detected (PLIP) ZN.8: 6 residues within 4Å: Chain A: E.123, W.127, M.164, A.165, C.168, H.212 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.123, A:M.164, A:H.212 ZN.9: 3 residues within 4Å: Chain A: P.8, H.196, E.198 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.196, A:E.198

1 x RET: RETINAL(Covalent)

RET.10: 18 residues within 4Å: Chain A: E.114, A.118, T.119, G.122, E.123, C.188, G.189, I.190, Y.192, M.208, H.212, F.213, F.262, W.266, Y.269, A.270, A.293, K.297 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.118, A:I.190, A:F.213, A:F.262, A:W.266, A:W.266, A:Y.269, A:Y.269, A:K.297

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

PLM.11: 6 residues within 4Å: Chain A: P.54, F.57, L.58, L.322, C.323 Ligands: PLM.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.54, A:F.57, A:L.58, A:L.322 PLM.12: 4 residues within 4Å: Chain A: L.322, C.323, C.324 Ligands: PLM.11 No protein-ligand interaction detected (PLIP) PLM.13: 6 residues within 4Å: Chain A: I.257, A.261, V.301, Y.302, V.305, I.306 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.261, A:V.301, A:Y.302, A:V.305, A:I.306

1 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)

HTG.14: 8 residues within 4Å: Chain A: L.267, P.268, G.271, V.272, Y.275, D.283, F.284, F.288 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.268, A:V.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okada, T. et al., The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J.Mol.Biol. (2004)

Release Date

2004-10-12

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Rhodopsin

Related Entries With Identical Sequence