- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 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
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 7 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)
BNG.3: 7 residues within 4Å:- Chain A: A.235, A.236, R.253, I.257, I.306, M.309
- Ligands: BNG.4
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:I.257, A:I.306
- Hydrogen bonds: A:R.253
- Salt bridges: A:R.253
BNG.4: 6 residues within 4Å:- Chain A: E.233, A.234, R.253, I.257, I.260
- Ligands: BNG.3
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:I.257, A:I.257, A:I.260
- Hydrogen bonds: A:E.233, A:R.253
- Salt bridges: A:R.253
BNG.5: 8 residues within 4Å:- Chain A: L.267, P.268, G.271, V.272, Y.275, D.283, F.288
- Ligands: BNG.7
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:V.272, A:Y.275, A:Y.275
BNG.6: 8 residues within 4Å:- Chain A: K.67, R.70, T.71, E.151, E.248, V.346, P.348
- Ligands: HTO.17
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:T.71
- Hydrogen bonds: A:E.151
BNG.7: 9 residues within 4Å:- Chain A: F.14, Y.31, L.32, E.34, G.285, P.286, I.287, F.288
- Ligands: BNG.5
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.287, A:F.288
- Hydrogen bonds: A:Y.31
BNG.25: 2 residues within 4Å:- Chain B: E.34, W.36
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.34
BNG.26: 7 residues within 4Å:- Chain B: Y.275, D.283, F.284, G.285, P.286, I.287, F.288
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.284, B:P.286, B:I.287, B:I.287
- 6 x HG: MERCURY (II) ION(Non-covalent)
HG.8: 4 residues within 4Å:- Chain A: C.265, F.295, T.298, Y.302
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:C.265
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: 3 residues within 4Å:- Chain A: Q.313, C.317, V.338
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:C.317
HG.27: 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.28: 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.29: 4 residues within 4Å:- Chain B: H.66, K.67, K.68, C.317
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.66, B:C.317
- 7 x ZN: ZINC ION(Non-covalent)
ZN.11: 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.12: 5 residues within 4Å:- Chain A: K.312, R.315, N.316, G.330, D.331
No protein-ligand interaction detected (PLIP)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: 4 residues within 4Å:- Chain A: P.8, H.196, E.198
- Ligands: NAG-NAG.24
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.196, A:E.198, A:E.198
ZN.30: 4 residues within 4Å:- Chain B: P.8, H.196, E.198
- Ligands: NAG-NAG.2
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.196, B:E.198, B:E.198
ZN.31: 4 residues within 4Å:- Chain A: E.197
- Chain B: E.202, F.277, Q.280
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Metal complexes: A:E.197, A:E.197, B:E.202, B:E.202
ZN.32: 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
- 4 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.15: 4 residues within 4Å:- Chain A: L.51, T.298, V.301, Y.302
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.51
HTO.16: 3 residues within 4Å:- Chain A: S.39, A.43, L.100
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.100
HTO.17: 4 residues within 4Å:- Chain A: A.247, S.335, T.336
- Ligands: BNG.6
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:A.247
- Hydrogen bonds: A:S.335, A:T.336
HTO.18: 5 residues within 4Å:- Chain A: M.318, V.319, L.322, L.329
- Ligands: PLM.21
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.329
- 5 x PLM: PALMITIC ACID(Non-covalent)(Covalent)
PLM.19: 3 residues within 4Å:- Chain A: L.41, Y.44, I.291
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.41, A:Y.44, A:I.291
PLM.21: 7 residues within 4Å:- Chain A: P.54, F.57, L.58, L.322, C.323
- Ligands: HTO.18, PLM.22
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.57, A:L.58, A:L.322
PLM.22: 4 residues within 4Å:- Chain A: L.322, C.323, C.324
- Ligands: PLM.21
No protein-ligand interaction detected (PLIP)PLM.33: 3 residues within 4Å:- Chain B: Y.44, L.51, Y.302
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.44, B:L.51, B:Y.302
PLM.35: 3 residues within 4Å:- Chain B: L.322, C.323, K.326
No protein-ligand interaction detected (PLIP)- 2 x RET: RETINAL(Covalent)
RET.20: 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
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:A.118, A:T.119, A:I.190, A:F.213, A:F.213, A:F.262, A:W.266, A:W.266, A:Y.269, A:A.270, A:K.297
RET.34: 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
12 PLIP interactions:12 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:Y.269, B:Y.269, B:A.270, B:K.297
- 1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-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
- Okada, T. et al., Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc.Natl.Acad.Sci.USA (2002)
- Release Date
- 2002-05-15
- 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- MAN: alpha-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(Non-covalent)
- 7 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)
- 6 x HG: MERCURY (II) ION(Non-covalent)
- 7 x ZN: ZINC ION(Non-covalent)
- 4 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 5 x PLM: PALMITIC ACID(Non-covalent)(Covalent)
- 2 x RET: RETINAL(Covalent)
- 1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-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
- Okada, T. et al., Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc.Natl.Acad.Sci.USA (2002)
- Release Date
- 2002-05-15
- Peptides
- rhodopsin: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.