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

Crystallographic model of 9-cis-rhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

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: 5 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21 No protein-ligand interaction detected (PLIP)

2 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) NAG-NAG.4: 6 residues within 4Å: Chain B: X.1, M.2, N.3, G.281, S.282, D.283 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-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(Post Translational Modification)

NAG-NAG-BMA-BMA.3: 6 residues within 4Å: Chain B: T.5, F.10, N.16, G.19, V.21, R.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.22

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

HG.5: 4 residues within 4Å: Chain A: A.261, C.265, T.298, Y.302 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.265 HG.6: 3 residues within 4Å: Chain A: A.133, C.223, Y.224 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.223 HG.7: 4 residues within 4Å: Chain A: Q.313, N.316, C.317, V.338 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.317, H2O.2 HG.18: 4 residues within 4Å: Chain B: A.261, C.265, T.298, Y.302 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.265, H2O.4, H2O.5 HG.19: 3 residues within 4Å: Chain B: A.133, C.223, Y.224 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.223, B:C.223 HG.20: 5 residues within 4Å: Chain B: H.66, C.317, T.337, V.338, S.339 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.66, B:C.317, B:T.337, B:V.338

7 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 4 residues within 4Å: Chain A: K.312, G.330, D.331 Chain B: H.101 No protein-ligand interaction detected (PLIP) ZN.10: 5 residues within 4Å: Chain A: E.123, W.127, M.164, A.165, H.212 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.123, A:M.164, A:H.212 ZN.11: 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.21: 3 residues within 4Å: Chain B: P.8, H.196, E.198 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.196, B:E.198 ZN.22: 3 residues within 4Å: Chain B: E.202, F.277, Q.280 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.202, B:E.202 ZN.23: 6 residues within 4Å: Chain B: E.123, W.127, M.164, A.165, C.168, H.212 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:M.164, B:H.212

2 x RET: RETINAL(Covalent)

RET.12: 18 residues within 4Å: Chain A: E.114, 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 10 PLIP interactions: 10 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:Y.269, A:A.270, A:K.297 RET.24: 18 residues within 4Å: Chain B: E.114, 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.118, B:T.119, B:I.190, B:F.213, B:F.262, B:W.266, B:W.266, B:Y.269, B:K.297

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

PLM.13: 7 residues within 4Å: Chain A: F.57, L.322, C.323 Chain B: M.50, F.53, F.89 Ligands: PLM.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.53, A:F.57 PLM.14: 6 residues within 4Å: Chain A: L.322, C.323, C.324 Chain B: V.82, F.89 Ligands: PLM.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.82, B:F.89 PLM.15: 8 residues within 4Å: Chain A: L.51, V.301, Y.302, V.305 Chain B: M.40, L.47 Ligands: HTG.17, PLM.28 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.47, A:L.51, A:Y.302, A:V.305 PLM.25: 7 residues within 4Å: Chain A: F.46, I.49, M.50 Chain B: L.322, C.323 Ligands: PLM.26, HTG.30 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.46, A:I.49 PLM.26: 6 residues within 4Å: Chain A: F.86, F.89 Chain B: L.322, C.323, C.324 Ligands: PLM.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.86, A:F.89 PLM.28: 8 residues within 4Å: Chain B: M.40, Y.44, L.47, L.51, V.301, Y.302, V.305 Ligands: PLM.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.44, B:L.47, B:L.51, B:V.301, B:Y.302, B:V.305

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

HTG.16: 6 residues within 4Å: Chain A: P.268, V.272, Y.275, D.283, F.284, F.288 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.268 HTG.17: 11 residues within 4Å: Chain A: R.253, I.257, V.305, I.306, M.309, M.310 Chain B: W.36, S.39, M.40, A.43 Ligands: PLM.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.36, B:A.43, A:V.305, A:I.306 Hydrogen bonds: B:S.39, A:M.310 HTG.29: 4 residues within 4Å: Chain B: Y.275, D.283, F.284, F.288 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.285 HTG.30: 11 residues within 4Å: Chain A: L.100, H.101 Chain B: K.312, R.315, N.316, M.318, L.322, G.330, D.331 Ligands: PLM.25, HTO.27 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.322, A:L.100 Hydrogen bonds: B:K.312, B:R.315, B:N.316, B:D.331, B:D.331, A:H.101

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

HTO.27: 7 residues within 4Å: Chain A: S.39, A.42, L.100 Chain B: I.308, M.309, R.315 Ligands: HTG.30 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.42, A:L.100 Hydrogen bonds: B:M.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamichi, H. et al., Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography. Biophys.J. (2007)

Release Date

2007-10-30

Peptides

Rhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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