SMTL ID : 1l9h.4 (3 other biounits)

Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION

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

NAG-NAG-MAN.1: 4 residues within 4Å: Chain A: T.5, 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(Non-covalent)

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

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(Non-covalent)

NAG-NAG-MAN-MAN.3: 4 residues within 4Å: Chain B: T.5, N.16, G.19, V.21 No protein-ligand interaction detected (PLIP)

7 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.5: 13 residues within 4Å: Chain A: A.235, A.236, R.253, I.257, I.306, M.309 Chain B: P.35, W.36, S.39, M.40, A.43, L.100 Ligands: BNG.6 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.36, B:A.43, A:I.257, A:I.306 Hydrogen bonds: B:S.39, B:L.100, A:R.253 Salt bridges: A:R.253 BNG.6: 8 residues within 4Å: Chain A: E.233, A.234, R.253, I.257, I.260 Chain B: W.36 Ligands: BNG.5, BNG.25 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.36, A:I.257, A:I.257, A:I.260 Hydrogen bonds: A:E.233, A:R.253 Salt bridges: A:R.253 BNG.7: 8 residues within 4Å: Chain A: L.267, P.268, G.271, V.272, Y.275, D.283, F.288 Ligands: BNG.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.272, A:Y.275, A:Y.275 BNG.8: 8 residues within 4Å: Chain A: K.67, R.70, T.71, E.151, E.248, V.346, P.348 Ligands: HTO.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.71 Hydrogen bonds: A:E.151 BNG.9: 9 residues within 4Å: Chain A: F.14, Y.31, L.32, E.34, G.285, P.286, I.287, F.288 Ligands: BNG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.287, A:F.288 Hydrogen bonds: A:Y.31 BNG.25: 4 residues within 4Å: Chain A: I.264 Chain B: E.34, W.36 Ligands: BNG.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.34 Hydrophobic interactions: A:I.264 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.10: 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.11: 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.12: 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.13: 3 residues within 4Å: Chain A: E.202, F.277, Q.280 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.202, A:E.202 ZN.14: 7 residues within 4Å: Chain A: K.312, R.315, N.316, G.330, D.331 Chain B: Y.97, H.101 No protein-ligand interaction detected (PLIP) ZN.15: 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.16: 3 residues within 4Å: Chain A: P.8, H.196, E.198 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.196, A:E.198, A:E.198 ZN.30: 3 residues within 4Å: Chain B: P.8, H.196, E.198 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.196, B:E.198, B:E.198 ZN.31: 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.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.17: 6 residues within 4Å: Chain A: L.51, T.298, V.301, Y.302 Chain B: L.47 Ligands: PLM.33 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.51, B:L.47 HTO.18: 5 residues within 4Å: Chain A: S.39, A.43, L.100 Chain B: M.309, R.315 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.100 HTO.19: 4 residues within 4Å: Chain A: A.247, S.335, T.336 Ligands: BNG.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.247 Hydrogen bonds: A:S.335, A:T.336 HTO.20: 9 residues within 4Å: Chain A: M.318, V.319, L.322, L.329 Chain B: F.46, I.49, T.93, Y.97 Ligands: PLM.23 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.93, B:Y.97, A:L.329

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

PLM.21: 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.23: 9 residues within 4Å: Chain A: P.54, F.57, L.58, L.322, C.323 Chain B: M.50, F.89 Ligands: HTO.20, PLM.24 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.89, A:F.57, A:L.58, A:L.322 PLM.24: 8 residues within 4Å: Chain A: L.322, C.323, C.324 Chain B: V.82, L.85, F.86, F.89 Ligands: PLM.23 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.82, B:L.85, B:L.85, B:F.86, B:F.89, B:F.89 PLM.33: 4 residues within 4Å: Chain B: Y.44, L.51, Y.302 Ligands: HTO.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.44, B:L.51, B:Y.302 PLM.35: 7 residues within 4Å: Chain A: F.46, I.49, M.50, F.53 Chain B: L.322, C.323, K.326 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.46, A:I.49, A:F.53

2 x RET: RETINAL(Covalent)

RET.22: 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

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
A

B
B

Membrane

We predict this structure to be a membrane protein.
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rhodopsin

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