- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.95 Å
- Oligo State
- homo-dimer
- Ligands
- 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
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 6 x HG: MERCURY (II) ION(Non-covalent)
HG.3: 4 residues within 4Å:- Chain A: A.261, C.265, T.298, Y.302
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:C.265, H2O.2, H2O.2
HG.4: 3 residues within 4Å:- Chain A: A.133, C.223, Y.224
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:C.223, A:C.223
HG.5: 5 residues within 4Å:- Chain A: H.66, C.317, T.337, V.338, S.339
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:H.66, A:C.317, A:T.337, A:V.338
HG.18: 4 residues within 4Å:- Chain B: A.261, C.265, T.298, Y.302
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:C.265
HG.19: 3 residues within 4Å:- Chain B: A.133, C.223, Y.224
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:C.223
HG.20: 4 residues within 4Å:- Chain B: Q.313, N.316, C.317, V.338
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.317, H2O.4
- 7 x ZN: ZINC ION(Non-covalent)
ZN.6: 4 residues within 4Å:- Chain A: P.8, H.196, E.198
- Ligands: NAG-NAG.17
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.196, A:E.198
ZN.7: 4 residues within 4Å:- Chain A: E.202, F.277, Q.280
- Chain B: E.197
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain A- Metal complexes: B:E.197, B:E.197, A:E.202, A:E.202
ZN.8: 6 residues within 4Å:- Chain A: E.123, W.127, M.164, A.165, C.168, H.212
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:M.164, A:H.212
ZN.21: 3 residues within 4Å:- Chain A: E.197
- Chain B: E.202, Q.280
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain A- Metal complexes: B:E.202, B:E.202, A:E.197, A:E.197
ZN.22: 3 residues within 4Å:- Chain B: K.312, G.330, D.331
No protein-ligand interaction detected (PLIP)ZN.23: 5 residues within 4Å:- Chain B: E.123, W.127, M.164, A.165, H.212
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:E.123, B:M.164, B:H.212
ZN.24: 2 residues within 4Å:- Chain B: H.196, E.198
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.196, B:E.198
- 2 x RET: RETINAL(Covalent)
RET.9: 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
9 PLIP interactions:9 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:K.297
RET.25: 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
10 PLIP interactions:10 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:A.270, B:K.297
- 6 x PLM: PALMITIC ACID(Covalent)(Non-covalent)
PLM.10: 4 residues within 4Å:- Chain A: L.322, C.323
- Ligands: PLM.11, HTG.15
No protein-ligand interaction detected (PLIP)PLM.11: 4 residues within 4Å:- Chain A: L.322, C.323, C.324
- Ligands: PLM.10
No protein-ligand interaction detected (PLIP)PLM.13: 7 residues within 4Å:- Chain A: M.40, Y.44, L.47, L.51, V.301, Y.302, V.305
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.44, A:L.47, A:L.51, A:V.301, A:Y.302, A:V.305
PLM.26: 4 residues within 4Å:- Chain B: F.57, L.322, C.323
- Ligands: PLM.27
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:F.57
PLM.27: 4 residues within 4Å:- Chain B: L.322, C.323, C.324
- Ligands: PLM.26
No protein-ligand interaction detected (PLIP)PLM.28: 5 residues within 4Å:- Chain B: L.51, V.301, Y.302, V.305
- Ligands: HTG.30
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.51, B:Y.302, B:V.305
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
HTG.14: 4 residues within 4Å:- Chain A: Y.275, D.283, F.284, F.288
1 PLIP interactions:1 interactions with chain A- Water bridges: A:G.285
HTG.15: 9 residues within 4Å:- Chain A: K.312, R.315, N.316, M.318, L.322, G.330, D.331
- Ligands: PLM.10, HTO.12
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:L.322
- Hydrogen bonds: A:K.312, A:R.315, A:N.316, A:D.331, A:D.331
HTG.29: 6 residues within 4Å:- Chain B: P.268, V.272, Y.275, D.283, F.284, F.288
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:P.268
HTG.30: 7 residues within 4Å:- Chain B: R.253, I.257, V.305, I.306, M.309, M.310
- Ligands: PLM.28
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.305, B:I.306
- Hydrogen bonds: B:M.310
- 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
- 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
BB
A - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.95 Å
- Oligo State
- homo-dimer
- Ligands
- 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
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 6 x HG: MERCURY (II) ION(Non-covalent)
- 7 x ZN: ZINC ION(Non-covalent)
- 2 x RET: RETINAL(Covalent)
- 6 x PLM: PALMITIC ACID(Covalent)(Non-covalent)
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
- 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
- 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
BB
A - Membrane
-
We predict this structure to be a membrane protein.