SMTL ID : 1gzm.1

Structure of Bovine Rhodopsin in a Trigonal Crystal Form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: E.114, A.118, T.119, G.122, E.123, C.188, G.189, I.190, Y.192, M.208, F.213, F.262, W.266, Y.269, A.293, K.297 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.118, A:T.119, A:I.190, A:F.213, A:F.262, A:W.266, A:Y.269, A:Y.269, A:K.297 RET.19: 17 residues within 4Å: Chain B: E.114, A.118, T.119, G.122, E.123, S.187, C.188, G.189, I.190, Y.192, M.208, F.213, F.262, W.266, Y.269, A.293, K.297 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.118, B:I.190, B:F.213, B:F.262, B:W.266, B:Y.269, B:Y.269, B:K.297

4 x PLM: PALMITIC ACID(Covalent)

PLM.2: 6 residues within 4Å: Chain A: L.51, P.54, I.55, L.322, C.323 Ligands: C8E.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.51, A:P.54, A:I.55 PLM.3: 8 residues within 4Å: Chain A: F.53, F.57, L.58, Y.61, T.321, L.322, C.323, C.324 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.53, A:L.58, A:Y.61, A:L.322 PLM.20: 4 residues within 4Å: Chain B: P.54, I.55, L.322, C.323 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.54, B:I.55, B:L.322 PLM.21: 6 residues within 4Å: Chain B: F.53, F.57, T.321, L.322, C.323, C.324 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.53, B:F.53, B:F.57

8 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.4: 5 residues within 4Å: Chain A: T.5, N.16, G.19, V.21 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.21 NAG.5: 3 residues within 4Å: Chain A: R.22 Ligands: NAG.4, BMA.6 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain A: X.1, N.3, G.281, D.283 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.281, A:D.283, A:D.283 NAG.8: 2 residues within 4Å: Ligands: NAG.7, BMA.9 No protein-ligand interaction detected (PLIP) NAG.22: 5 residues within 4Å: Chain B: T.5, N.16, G.19, V.21 Ligands: NAG.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.16, B:V.21, B:R.22 NAG.23: 2 residues within 4Å: Ligands: NAG.22, BMA.24 No protein-ligand interaction detected (PLIP) NAG.25: 6 residues within 4Å: Chain B: X.1, M.2, N.3, G.281, D.283 Ligands: NAG.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.283, B:D.283 NAG.26: 2 residues within 4Å: Ligands: NAG.25, BMA.27 No protein-ligand interaction detected (PLIP)

4 x BMA: BETA-D-MANNOSE(Non-functional Binders)

BMA.6: 1 residues within 4Å: Ligands: NAG.5 No protein-ligand interaction detected (PLIP) BMA.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP) BMA.24: 1 residues within 4Å: Ligands: NAG.23 No protein-ligand interaction detected (PLIP) BMA.27: 1 residues within 4Å: Ligands: NAG.26 No protein-ligand interaction detected (PLIP)

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.10: 7 residues within 4Å: Chain A: I.257, A.261, I.264, T.298, Y.302, V.305, I.306 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.257, A:A.261, A:I.264, A:Y.302, A:V.305, A:I.306 PEF.30: 5 residues within 4Å: Chain B: A.261, T.298, Y.302, I.306, M.310 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.261, B:Y.302, B:I.306

3 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.11: 8 residues within 4Å: Chain A: F.213, L.267, G.271, V.272, F.274, Y.275, F.288 Ligands: C8E.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.213, A:F.274 LDA.31: 7 residues within 4Å: Chain B: F.209, F.213, L.267, G.271, V.272, F.274 Ligands: LDA.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.209, B:F.213, B:F.274, B:F.274 LDA.36: 8 residues within 4Å: Chain B: L.267, P.268, G.271, V.272, Y.275, F.288 Ligands: C8E.28, LDA.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.267, B:P.268

12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.12: 6 residues within 4Å: Chain A: L.41, Y.44, P.268, I.291, P.292, F.295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.41, A:Y.44, A:P.268 C8E.13: 4 residues within 4Å: Chain A: T.109, N.112, F.116, L.173 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.112, A:F.116, A:L.173 Hydrogen bonds: A:N.112 C8E.14: 5 residues within 4Å: Chain A: F.221, Y.224, I.260 Chain B: T.278 Ligands: C8E.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.221 C8E.15: 6 residues within 4Å: Chain A: I.308, M.309, R.315, N.316, M.318 Ligands: PLM.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.308 Hydrogen bonds: A:R.315 C8E.16: 4 residues within 4Å: Chain A: F.274, Y.275 Chain B: L.263 Ligands: LDA.11 No protein-ligand interaction detected (PLIP) C8E.17: 2 residues within 4Å: Chain A: F.222 Chain B: V.210 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.210 C8E.28: 8 residues within 4Å: Chain A: I.260, L.263 Chain B: F.274, Y.275, T.278, H.279 Ligands: C8E.14, LDA.36 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.260 Hydrogen bonds: B:F.274, B:T.278 C8E.29: 3 residues within 4Å: Chain A: Y.207 Chain B: I.218, F.222 No protein-ligand interaction detected (PLIP) C8E.32: 4 residues within 4Å: Chain B: Y.44, I.291, P.292, F.295 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.291 C8E.33: 3 residues within 4Å: Chain B: T.109, N.112, F.116 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.112, B:F.116, B:F.116 Hydrogen bonds: B:N.112 C8E.34: 3 residues within 4Å: Chain A: T.278 Chain B: Y.224, I.260 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.278, B:Y.224 C8E.35: 4 residues within 4Å: Chain B: I.308, R.315, N.316, M.318 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.308 Hydrogen bonds: B:R.315

2 x ZN: ZINC ION(Non-covalent)

ZN.18: 5 residues within 4Å: Chain A: R.148, G.150, E.151, N.152, H.153 No protein-ligand interaction detected (PLIP) ZN.37: 4 residues within 4Å: Chain B: R.148, G.150, N.152, H.153 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structure of Bovine Rhodopsin in a Trigonal Crystal Form. J.Mol.Biol. (2004)

Release Date

2003-11-20

Peptides

RHODOPSIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RHODOPSIN

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