SMTL ID : 3cap.1

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 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(Non-functional Binders)

NAG-NAG-BMA-BMA.1: 5 residues within 4Å: Chain A: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.3: 4 residues within 4Å: Chain B: N.15, G.18, V.20, R.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.21

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

NAG-NAG.2: 4 residues within 4Å: Chain A: M.1, N.2, G.280, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: M.1, N.2, G.280, D.282 No protein-ligand interaction detected (PLIP)

6 x BGL: 2-O-octyl-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

BGL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BGL.6: 3 residues within 4Å: Chain A: E.33, W.35, Q.36 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.33 Hydrogen bonds: A:Q.36 BGL.7: 5 residues within 4Å: Chain A: F.220, G.224, K.231, T.251, V.254 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.220, A:F.220, A:V.254 Hydrogen bonds: A:K.231 Salt bridges: A:K.231 BGL.8: 3 residues within 4Å: Chain A: Y.96, H.100 Chain B: W.35 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.35, B:W.35, B:W.35, A:Y.96 BGL.10: 5 residues within 4Å: Chain A: P.34, W.35 Chain B: Y.96, L.99, H.100 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.35, A:W.35, B:Y.96, B:Y.96, B:L.99 BGL.11: 2 residues within 4Å: Chain B: Q.36, M.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.36

2 x PLM: PALMITIC ACID(Covalent)

PLM.9: 7 residues within 4Å: Chain A: L.321, C.322 Chain B: I.256, T.297, Y.301, V.304, M.309 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.256, B:Y.301, B:V.304 PLM.12: 5 residues within 4Å: Chain A: I.256, T.297, Y.301, M.309 Chain B: C.322 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.326 Hydrophobic interactions: A:I.256, A:Y.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.H. et al., Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature (2008)

Release Date

2008-06-24

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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