- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 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
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:C.265
HG.4: 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.5: 5 residues within 4Å:- Chain A: H.66, C.317, T.337, V.338, S.339
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:C.317, A:T.337, A:V.338
HG.19: 5 residues within 4Å:- Chain B: A.261, C.265, F.295, T.298, Y.302
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:C.265
HG.20: 4 residues within 4Å:- Chain B: A.133, C.223, Y.224, L.227
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:C.223
HG.21: 5 residues within 4Å:- Chain B: Q.313, N.316, C.317, T.337, V.338
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.317, H2O.3
- 7 x ZN: ZINC ION(Non-covalent)
ZN.6: 4 residues within 4Å:- Chain A: P.8, H.196, E.198
- Ligands: NAG-NAG.18
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.196, A:E.198, 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 A, 2 interactions with chain B- Metal complexes: A:E.202, A:E.202, B:E.197, B:E.197
ZN.8: 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.22: 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.23: 3 residues within 4Å:- Chain B: K.312, G.330, D.331
No protein-ligand interaction detected (PLIP)ZN.24: 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
ZN.25: 4 residues within 4Å:- Chain B: P.8, H.196, E.198
- Ligands: NAG-NAG.2
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.196, B:E.198
- 2 x RET: RETINAL(Covalent)
RET.9: 17 residues within 4Å:- Chain A: A.118, T.119, G.122, E.123, E.182, S.187, C.188, I.190, Y.192, M.208, F.213, F.262, W.266, Y.269, A.270, A.293, K.297
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:I.190, A:F.213, A:F.262, A:W.266, A:Y.269, A:Y.269, A:A.293, A:K.297
RET.26: 16 residues within 4Å:- Chain B: A.118, T.119, G.122, E.123, S.187, I.190, Y.192, M.208, H.212, F.213, F.262, W.266, Y.269, A.270, A.293, K.297
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:A.118, B:I.190, B:F.213, B:F.262, B:W.266, B:W.266, B:Y.269, B:Y.269, B:Y.269, B:A.293, B:K.297
- 6 x PLM: PALMITIC ACID(Covalent)(Non-covalent)
PLM.10: 5 residues within 4Å:- Chain A: P.54, L.58, L.322, C.323
- Ligands: PLM.11
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:P.54, A:L.58, A:L.322
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: 4 residues within 4Å:- Chain A: M.40, L.47, V.301, Y.302
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.47, A:V.301, A:Y.302
PLM.27: 6 residues within 4Å:- Chain B: P.54, F.57, L.58, L.322, C.323
- Ligands: PLM.28
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:P.54, B:F.57, B:L.58, B:L.322, B:L.322, B:L.322
PLM.28: 4 residues within 4Å:- Chain B: L.322, C.323, C.324
- Ligands: PLM.27
No protein-ligand interaction detected (PLIP)PLM.29: 6 residues within 4Å:- Chain B: I.257, A.261, V.301, Y.302, V.305, I.306
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:A.261, B:V.301, B:Y.302, B:V.305, B:I.306, B:I.306
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
HTG.14: 5 residues within 4Å:- Chain A: P.268, Y.275, D.283, F.284, F.288
1 PLIP interactions:1 interactions with chain A- Water bridges: A:G.285
HTG.15: 5 residues within 4Å:- Chain A: P.35, W.36, S.39, M.40, A.43
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.36, A:A.43
- Hydrogen bonds: A:S.39
HTG.16: 7 residues within 4Å:- Chain A: K.312, R.315, N.316, L.322, G.330, D.331
- Ligands: HTO.12
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:R.315, A:L.322
- Hydrogen bonds: A:K.312, A:R.315, A:N.316, A:D.331, A:D.331, A:D.331
HTG.30: 7 residues within 4Å:- Chain B: L.267, P.268, G.271, V.272, Y.275, F.284, F.288
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.272
- 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., Crystallographic analysis of primary visual photochemistry. Angew.Chem.Int.Ed.Engl. (2006)
- Release Date
- 2006-09-02
- 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 2.60 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., Crystallographic analysis of primary visual photochemistry. Angew.Chem.Int.Ed.Engl. (2006)
- Release Date
- 2006-09-02
- Peptides
- Rhodopsin: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
A - Membrane
-
We predict this structure to be a membrane protein.