- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x NAG- NAG- BMA: 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)
- 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)
- 2 x RET: RETINAL(Covalent)
- 4 x PLM: PALMITIC ACID(Covalent)
PLM.6: 8 residues within 4Å:- Chain A: F.57, L.58, L.322, C.323
- Chain B: M.50, F.53, F.89
- Ligands: PLM.7
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:F.57, A:L.322, B:F.53
PLM.7: 4 residues within 4Å:- Chain A: L.322, C.323, C.324
- Ligands: PLM.6
No protein-ligand interaction detected (PLIP)PLM.20: 6 residues within 4Å:- Chain A: F.46, I.49, M.50
- Chain B: C.323
- Ligands: PLM.21, HTG.31
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.46, A:I.49
PLM.21: 5 residues within 4Å:- Chain A: F.89
- Chain B: L.322, C.323, C.324
- Ligands: PLM.20
No protein-ligand interaction detected (PLIP)- 6 x HG: MERCURY (II) ION(Non-covalent)
HG.8: 4 residues within 4Å:- Chain A: C.265, F.295, T.298, Y.302
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:C.265, A:T.298
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: 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
HG.22: 4 residues within 4Å:- Chain B: A.261, C.265, T.298, Y.302
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.265, H2O.5
HG.23: 3 residues within 4Å:- Chain B: C.223, Y.224, L.227
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:C.223, B:C.223
HG.24: 6 residues within 4Å:- Chain B: Q.313, N.316, C.317, E.333, T.337, V.338
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:C.317
- 7 x ZN: ZINC ION(Non-covalent)
ZN.11: 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.12: 3 residues within 4Å:- Chain A: K.312, D.331
- Chain B: H.101
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Metal complexes: A:D.331, B:H.101
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: 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.25: 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
ZN.26: 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.27: 6 residues within 4Å:- Chain B: E.123, W.127, M.164, A.165, C.168, H.212
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:E.123, B:M.164, B:H.212
- 2 x 4E6: (4E,6E)-hexadeca-1,4,6-triene(Non-covalent)
4E6.15: 8 residues within 4Å:- Chain A: L.47, L.51, I.257, T.298, V.301, Y.302
- Chain B: L.47
- Ligands: HTG.17
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.47, A:I.257, A:T.298, A:Y.302
4E6.29: 6 residues within 4Å:- Chain B: M.40, Y.44, L.47, L.51, Y.302, V.305
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:Y.44, B:L.47, B:L.51, 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, G.271, Y.275, F.284, F.288
- Ligands: ID3.18
No protein-ligand interaction detected (PLIP)HTG.17: 9 residues within 4Å:- Chain A: I.257, I.306, M.309, M.310
- Chain B: P.35, W.36, S.39, A.43
- Ligands: 4E6.15
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain B- Hydrophobic interactions: A:I.306, B:W.36, B:A.43
- Hydrogen bonds: A:M.310, B:S.39
HTG.30: 5 residues within 4Å:- Chain B: V.272, Y.275, F.284, F.288
- Ligands: ID3.32
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:V.272
- Hydrogen bonds: B:D.283
HTG.31: 9 residues within 4Å:- Chain A: L.100, H.101
- Chain B: K.312, R.315, N.316, M.318, D.331
- Ligands: PLM.20, HTO.28
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:K.312, B:R.315, B:N.316, B:D.331, A:H.101
- Hydrophobic interactions: A:L.100
- 2 x ID3: (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one(Non-covalent)
ID3.18: 5 residues within 4Å:- Chain A: G.285, P.286, I.287, F.288
- Ligands: HTG.16
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.287, A:F.288, A:F.288
ID3.32: 6 residues within 4Å:- Chain B: D.283, F.284, G.285, I.287, F.288
- Ligands: HTG.30
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:I.287
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 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: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x NAG- NAG- BMA: 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)
- 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)
- 2 x RET: RETINAL(Covalent)
- 4 x PLM: PALMITIC ACID(Covalent)
- 6 x HG: MERCURY (II) ION(Non-covalent)
- 7 x ZN: ZINC ION(Non-covalent)
- 2 x 4E6: (4E,6E)-hexadeca-1,4,6-triene(Non-covalent)
- 4 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
- 2 x ID3: (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one(Non-covalent)
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 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: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.