SMTL ID : 3oax.2 (2 other biounits)

Crystal structure of bovine rhodopsin with beta-ionone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Covalent)

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: T.5, F.10, 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: 5 residues within 4Å: Chain A: M.2, N.3, G.281, S.282, D.283 No protein-ligand interaction detected (PLIP)

1 x RET: RETINAL(Covalent)

RET.3: 19 residues within 4Å: Chain A: E.114, A.118, T.119, G.122, E.123, S.187, 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 10 PLIP interactions: 10 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:A.270, A:K.297

2 x PLM: PALMITIC ACID(Covalent)

PLM.4: 3 residues within 4Å: Chain A: C.323 Ligands: PLM.5, HTG.15 No protein-ligand interaction detected (PLIP) PLM.5: 4 residues within 4Å: Chain A: L.322, C.323, C.324 Ligands: PLM.4 No protein-ligand interaction detected (PLIP)

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

HG.6: 4 residues within 4Å: Chain A: A.261, C.265, T.298, Y.302 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.265, H2O.2 HG.7: 3 residues within 4Å: Chain A: C.223, Y.224, L.227 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.223, A:C.223 HG.8: 6 residues within 4Å: Chain A: Q.313, N.316, C.317, E.333, T.337, V.338 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.317

3 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain A: H.196, E.198 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.196, A:E.198 ZN.10: 3 residues within 4Å: Chain A: E.202, F.277, Q.280 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.202, A:E.202 ZN.11: 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

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

HTO.12: 4 residues within 4Å: Chain A: I.308, M.309, R.315 Ligands: HTG.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.309

1 x 4E6: (4E,6E)-hexadeca-1,4,6-triene(Non-covalent)

4E6.13: 6 residues within 4Å: Chain A: M.40, Y.44, L.47, L.51, Y.302, V.305 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.44, A:L.47, A:L.51, A:Y.302, A:V.305

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

HTG.14: 5 residues within 4Å: Chain A: V.272, Y.275, F.284, F.288 Ligands: ID3.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.272 Hydrogen bonds: A:D.283 HTG.15: 7 residues within 4Å: Chain A: K.312, R.315, N.316, M.318, D.331 Ligands: PLM.4, HTO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.312, A:R.315, A:N.316, A:D.331

1 x ID3: (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one(Non-covalent)

ID3.16: 6 residues within 4Å: Chain A: D.283, F.284, G.285, I.287, F.288 Ligands: HTG.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makino, C.L. et al., Binding of more than one retinoid to visual opsins. Biophys.J. (2010)

Release Date

2011-01-19

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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