SMTL ID : 1f88.1 (2 other biounits)

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: T.4, N.15, G.18, V.20, R.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 NAG-NAG.2: 5 residues within 4Å: Chain A: M.1, N.2, G.280, S.281, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.2, G.280, S.281, D.282 No protein-ligand interaction detected (PLIP)

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(Post Translational Modification)

NAG-NAG-MAN.3: 5 residues within 4Å: Chain B: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

6 x HG: MERCURY (II) ION(Non-covalent)

HG.5: 3 residues within 4Å: Chain A: C.264, T.297, Y.301 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.264 HG.6: 5 residues within 4Å: Chain A: A.132, R.135, C.222, Y.223, L.226 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.222 HG.7: 3 residues within 4Å: Chain A: Q.312, C.316, S.338 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.316 HG.11: 3 residues within 4Å: Chain B: A.260, C.264, T.297 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.264 HG.12: 4 residues within 4Å: Chain B: A.132, C.222, Y.223, L.226 No protein-ligand interaction detected (PLIP) HG.13: 2 residues within 4Å: Chain B: H.65, C.316 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.316

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain A: E.201, Q.279 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.201 ZN.9: 5 residues within 4Å: Chain A: K.311, R.314, N.315 Chain B: Y.96, H.100 No protein-ligand interaction detected (PLIP) ZN.14: 3 residues within 4Å: Chain B: E.201, F.276, Q.279 No protein-ligand interaction detected (PLIP) ZN.15: 3 residues within 4Å: Chain B: P.7, H.195, E.197 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:P.7, B:H.195

2 x RET: RETINAL(Covalent)

RET.10: 16 residues within 4Å: Chain A: E.113, A.117, T.118, G.121, E.122, S.186, C.187, I.189, M.207, F.212, F.261, W.265, Y.268, A.269, A.292, K.296 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.117, A:T.118, A:I.189, A:F.212, A:F.261, A:W.265, A:Y.268, A:Y.268, A:A.269, A:K.296 RET.16: 17 residues within 4Å: Chain B: E.113, A.117, T.118, G.121, E.122, C.187, G.188, I.189, Y.191, M.207, F.212, F.261, W.265, Y.268, A.269, A.292, K.296 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.117, B:T.118, B:I.189, B:F.212, B:F.261, B:W.265, B:W.265, B:W.265, B:Y.268, B:Y.268, B:Y.268, B:A.269, B:K.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palczewski, K. et al., Crystal structure of rhodopsin: A G protein-coupled receptor. Science (2000)

Release Date

2000-08-04

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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