SMTL ID : 1hzx.1 (3 other biounits)

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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: 5 residues within 4Å: Chain A: M.2, N.3, G.281, S.282, D.283 No protein-ligand interaction detected (PLIP)

5 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.3: 6 residues within 4Å: Chain A: A.235, A.236, R.253, I.257, I.306, M.309 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.257, A:I.306 Hydrogen bonds: A:A.236, A:R.253, A:M.309 Salt bridges: A:R.253 BNG.4: 5 residues within 4Å: Chain A: E.233, A.234, R.253, I.257, A.261 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.261 Hydrogen bonds: A:E.233, A:R.253 Salt bridges: A:R.253 BNG.5: 5 residues within 4Å: Chain A: L.267, P.268, V.272, Y.275, F.288 No protein-ligand interaction detected (PLIP) BNG.6: 8 residues within 4Å: Chain A: K.67, K.68, R.70, T.71, E.151, E.248, V.346, P.348 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.71 Hydrogen bonds: A:E.151 BNG.7: 8 residues within 4Å: Chain A: F.14, Y.31, L.32, E.34, G.285, P.286, I.287, F.288 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.287, A:I.287, A:F.288 Hydrogen bonds: A:Y.31

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

HG.8: 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.9: 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.10: 3 residues within 4Å: Chain A: Q.313, C.317, V.338 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.317

4 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: E.202, F.277, Q.280 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.202 ZN.12: 6 residues within 4Å: Chain A: K.312, R.315, N.316, L.329, G.330, D.331 No protein-ligand interaction detected (PLIP) ZN.13: 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.14: 5 residues within 4Å: Chain A: C.265, W.266, P.268, Y.269, P.292 No protein-ligand interaction detected (PLIP)

2 x PLM: PALMITIC ACID(Covalent)

PLM.15: 5 residues within 4Å: Chain A: P.54, L.322, C.323 Ligands: PLM.16, HTO.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.54, A:L.322 PLM.16: 4 residues within 4Å: Chain A: L.322, C.323, C.324 Ligands: PLM.15 No protein-ligand interaction detected (PLIP)

1 x RET: RETINAL(Covalent)

RET.17: 19 residues within 4Å: Chain A: E.114, G.115, A.118, T.119, G.122, E.123, S.187, C.188, I.190, Y.192, M.208, H.212, F.213, F.262, W.266, Y.269, A.270, A.293, K.297 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.118, A:T.119, A:I.190, A:F.213, A:F.262, A:W.266, A:W.266, A:W.266, A:W.266, A:Y.269, A:A.270, A:K.297

4 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.18: 4 residues within 4Å: Chain A: L.47, L.48, T.298, V.301 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.47 HTO.19: 4 residues within 4Å: Chain A: Y.44, I.291, F.294, F.295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.291, A:F.295 Hydrogen bonds: A:Y.44 HTO.20: 5 residues within 4Å: Chain A: A.247, E.250, Q.313, S.335, T.336 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.250 Hydrogen bonds: A:Q.313, A:S.335, A:T.336 HTO.21: 4 residues within 4Å: Chain A: M.318, V.319, L.329 Ligands: PLM.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teller, D.C. et al., Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry (2001)

Release Date

2001-07-04

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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