SMTL ID : 4ryy.1

Crystal structure of RPE65 in complex with R-emixustat and palmitate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.180, H.241, H.313, H.527 Ligands: PLM.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.180, A:H.241, A:H.313, A:H.527 FE2.4: 5 residues within 4Å: Chain B: H.180, H.241, H.313, H.527 Ligands: PLM.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.180, B:H.241, B:H.313, B:H.527

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 20 residues within 4Å: Chain A: L.60, F.61, V.134, H.180, H.241, F.312, H.313, W.331, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, H.527 Ligands: FE2.1, A3V.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.60, A:F.61, A:F.312, A:F.312, A:Y.338, A:L.341, A:F.418, A:L.437, A:L.439, A:P.444, A:V.524 Salt bridges: A:H.241, A:H.527 PLM.5: 21 residues within 4Å: Chain B: L.60, F.61, V.134, H.180, H.241, F.312, H.313, W.331, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, T.525, H.527 Ligands: FE2.4, A3V.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.60, B:F.61, B:F.312, B:W.331, B:Y.338, B:L.341, B:F.418, B:F.418, B:L.437, B:L.439, B:P.444, B:V.524 Salt bridges: B:H.241, B:H.527

2 x A3V: (1R)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol(Non-covalent)

A3V.3: 15 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, Y.239, H.241, I.259, Y.275, Y.338 Ligands: PLM.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.61, A:F.103, A:F.103, A:T.129, A:E.148, A:T.149, A:I.259 Hydrogen bonds: A:T.147, A:E.148, A:E.148 pi-Stacking: A:Y.275 A3V.6: 15 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, Y.239, H.241, I.259, Y.275, Y.338 Ligands: PLM.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.61, B:F.103, B:F.103, B:T.129, B:E.148, B:T.149, B:I.259 Hydrogen bonds: B:E.148, B:E.148, B:Y.338 pi-Stacking: B:Y.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Molecular pharmacodynamics of emixustat in protection against retinal degeneration. J.Clin.Invest. (2015)

Release Date

2015-05-27

Peptides

Retinoid isomerohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinoid isomerohydrolase

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