SMTL ID : 4pxf.1

Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-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

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 NAG-NAG-BMA-MAN.9: 6 residues within 4Å: Chain C: T.4, F.9, N.15, G.18, V.20, R.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.21

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.2: 4 residues within 4Å: Chain A: K.66, R.69, Y.74, E.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.66, A:K.66, A:R.69 Salt bridges: A:R.69 GLC-GLC.10: 4 residues within 4Å: Chain C: K.66, R.69, Y.74, E.150 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.66, C:K.66, C:R.69 Salt bridges: C:R.69

6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 5 residues within 4Å: Chain A: P.27, Y.96, L.99, H.100 Chain C: W.35 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.96, A:L.99, C:W.35, C:W.35, C:W.35 Hydrogen bonds: A:H.100 Salt bridges: A:H.100 BOG.4: 11 residues within 4Å: Chain A: T.118, G.121, E.122, Y.191, M.207, F.208, F.212, W.265, Y.268, A.269, A.272 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.191, A:Y.191, A:M.207, A:F.208, A:F.212, A:Y.268, A:A.272 Hydrogen bonds: A:E.122, A:E.122 Water bridges: A:E.181, A:K.296 BOG.5: 4 residues within 4Å: Chain A: W.35, Q.36, L.40, I.286 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.35 Hydrogen bonds: A:Q.36 BOG.11: 5 residues within 4Å: Chain A: W.35 Chain C: P.27, Y.96, L.99, H.100 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.96, C:L.99, A:W.35, A:W.35, A:W.35 Hydrogen bonds: C:H.100 Salt bridges: C:H.100 BOG.12: 11 residues within 4Å: Chain C: T.118, G.121, E.122, Y.191, M.207, F.208, F.212, W.265, Y.268, A.269, A.272 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.191, C:Y.191, C:M.207, C:F.208, C:F.212, C:Y.268, C:A.272 Hydrogen bonds: C:T.118, C:E.122 Water bridges: C:E.181, C:K.296 BOG.13: 4 residues within 4Å: Chain C: W.35, Q.36, L.40, I.286 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.35 Hydrogen bonds: C:Q.36

2 x PLM: PALMITIC ACID(Covalent)

PLM.6: 10 residues within 4Å: Chain A: L.321, C.322, C.323 Chain C: Y.43, R.252, I.256, T.297, Y.301, V.304 Ligands: ACT.8 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.256, C:T.297, C:V.304 Hydrogen bonds: C:R.252 PLM.14: 10 residues within 4Å: Chain A: Y.43, R.252, I.256, T.297, Y.301, V.304 Chain C: L.321, C.322, C.323 Ligands: ACT.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.256, A:T.297, A:V.304 Hydrogen bonds: A:R.252

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: G.284, P.285, I.286, F.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.284, A:I.286, A:F.287 SO4.15: 4 residues within 4Å: Chain C: G.284, P.285, I.286, F.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.284, C:I.286, C:F.287

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: M.49, L.50 Ligands: PLM.6 No protein-ligand interaction detected (PLIP) ACT.16: 3 residues within 4Å: Chain C: M.49, L.50 Ligands: PLM.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szczepek, M. et al., Crystal structure of a common GPCR-binding interface for G protein and arrestin. Nat Commun (2014)

Release Date

2014-09-17

Peptides

Rhodopsin: AC
S-arrestin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

S-arrestin

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