SMTL ID : 4ryx.1

Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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 FE2.8: 5 residues within 4Å: Chain B: H.180, H.241, H.313, H.527 Ligands: PLM.9 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, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, T.525, 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: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.313, A:H.527 PLM.9: 20 residues within 4Å: Chain B: L.60, F.61, V.134, H.180, H.241, F.312, H.313, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, T.525, H.527 Ligands: FE2.8, A3V.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.60, B:F.61, B:F.312, B:Y.338, B:L.341, B:F.418, B:L.437, B:L.439, B:P.444, B:V.524 Salt bridges: B:H.241, B:H.313, B:H.527

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

A3V.3: 14 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, Y.239, H.241, I.259, F.264, Y.275, F.279, Y.338 Ligands: PLM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.61, A:F.103, A:F.103, A:T.129, A:I.259, A:F.264, A:F.279 Hydrogen bonds: A:E.148, A:E.148 A3V.10: 14 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, Y.239, H.241, I.259, F.264, Y.275, F.279, Y.338 Ligands: PLM.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.61, B:F.103, B:F.103, B:T.129, B:I.259, B:F.264, B:F.279 Hydrogen bonds: B:T.147, B:E.148, B:E.148

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

SO4.4: 4 residues within 4Å: Chain A: R.33, P.35, L.36, W.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.36, A:W.37 Water bridges: A:W.37 Salt bridges: A:R.33 SO4.11: 4 residues within 4Å: Chain B: R.33, P.35, L.36, W.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.36, B:W.37 Water bridges: B:W.37 Salt bridges: B:R.33

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 9 residues within 4Å: Chain A: E.283, T.284, M.285, G.286, P.308, W.402 Chain B: C.396, W.402 Ligands: MPD.12 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.284, A:G.286 Hydrophobic interactions: B:W.402, B:W.402 MPD.6: 6 residues within 4Å: Chain A: W.37, H.475, G.484, V.485, N.506, V.513 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.485, A:N.506, A:V.513 MPD.7: 5 residues within 4Å: Chain B: V.407, L.408, F.409, K.455 Ligands: MPD.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:V.407, A:S.410 Hydrophobic interactions: B:K.455 MPD.12: 9 residues within 4Å: Chain A: C.396, W.402 Chain B: E.283, T.284, M.285, G.286, P.308, W.402 Ligands: MPD.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.284, B:G.286 Hydrophobic interactions: A:W.402, A:W.402 MPD.13: 6 residues within 4Å: Chain B: W.37, H.475, G.484, V.485, N.506, V.513 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.485, B:N.506, B:V.513 MPD.14: 5 residues within 4Å: Chain A: V.407, L.408, F.409, K.455 Ligands: MPD.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.455 Water bridges: B:V.407, B:S.410

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
A

Retinoid isomerohydrolase

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