SMTL ID : 4zhk.1

Crystal structure of RPE65 in complex with MB-002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: A9V.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.180, A:H.241, A:H.313, A:H.527, A9V.7 FE2.8: 5 residues within 4Å: Chain B: H.180, H.241, H.313, H.527 Ligands: A9V.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.180, B:H.241, B:H.313, B:H.527, A9V.13

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 8 residues within 4Å: Chain A: Q.4, V.5, V.459, W.460, Q.461, E.462, P.463 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.461 PG4.9: 7 residues within 4Å: Chain B: Q.4, V.5, V.459, W.460, Q.461, P.463 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.461

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: Q.461 Ligands: PG4.2 No protein-ligand interaction detected (PLIP) NA.10: 2 residues within 4Å: Chain B: Q.461 Ligands: PG4.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.461

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: D.320, P.430, Y.431, T.432, K.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.318 Water bridges: A:N.388, A:T.432 PGE.5: 4 residues within 4Å: Chain A: D.483, G.484, N.506, K.508 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.483, A:N.506 Water bridges: A:R.33 PGE.11: 6 residues within 4Å: Chain B: Y.318, D.320, P.430, Y.431, T.432, K.453 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.453

2 x A8V: (1S)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol(Non-covalent)

A8V.6: 15 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, F.196, Y.239, H.241, I.259, Y.275, Y.338 10 PLIP interactions: 10 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:F.196, A:I.259 Hydrogen bonds: A:T.147 pi-Stacking: A:Y.275 A8V.12: 15 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, F.196, Y.239, H.241, I.259, Y.275, Y.338 12 PLIP interactions: 12 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:F.196, B:I.259 Hydrogen bonds: B:E.148, B:Y.239, B:Y.338 pi-Stacking: B:Y.275

2 x A9V: (1R)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol(Non-covalent)

A9V.7: 16 residues within 4Å: Chain A: L.60, F.61, V.134, H.241, F.312, H.313, Y.338, L.341, E.417, F.418, L.439, F.442, P.444, V.524, H.527 Ligands: FE2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.60, A:F.312, A:F.312, A:F.418, A:P.444, A:V.524 Hydrogen bonds: A:H.241, A:Y.338 A9V.13: 16 residues within 4Å: Chain B: L.60, F.61, V.134, H.241, F.312, H.313, Y.338, L.341, E.417, F.418, L.439, F.442, P.444, V.524, H.527 Ligands: FE2.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.60, B:F.312, B:F.312, B:F.418, B:L.439, B:P.444, B:V.524 Hydrogen bonds: B:H.241

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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