SMTL ID : 5ulg.1

Crystal structure of RPE65 in complex with MB-008 and palmitate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 FE2.6: 5 residues within 4Å: Chain B: H.180, H.241, H.313, H.527 Ligands: PLM.7 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: 21 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, T.525, H.527 Ligands: FE2.1, 8E4.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.60, A:F.61, A:F.312, A:F.312, A:W.331, A:Y.338, A:L.341, A:F.418, A:L.437, A:P.444, A:V.524 Salt bridges: A:H.241, A:H.527 PLM.7: 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: FE2.6, 8E4.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.60, B:F.61, B:F.312, B:F.312, B:W.331, B:Y.338, B:L.341, B:F.418, B:L.437, B:L.439, B:V.524 Salt bridges: B:H.241, B:H.527

2 x 8E4: (3S)-3-({3-[(1R)-3-amino-1-hydroxypropyl]phenoxy}methyl)hexan-1-ol(Non-covalent)

8E4.3: 18 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, G.176, N.194, Y.239, H.241, I.259, F.264, Y.275, F.279, Y.338 Ligands: PLM.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.103, A:F.103, A:T.129, A:E.148, A:T.149, A:I.259, A:F.264, A:F.279 Hydrogen bonds: A:T.147, A:E.148, A:N.194 pi-Stacking: A:Y.275 8E4.8: 17 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, G.176, N.194, Y.239, H.241, F.264, Y.275, F.279, Y.338 Ligands: PLM.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.61, B:F.103, B:T.129, B:E.148, B:T.149, B:F.264, B:Y.275, B:F.279 Hydrogen bonds: B:E.148, B:N.194, B:Y.338 pi-Stacking: B:Y.275

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

PG4.4: 8 residues within 4Å: Chain A: Q.4, V.5, V.459, W.460, Q.461, E.462, P.463 Ligands: NA.5 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.5: 2 residues within 4Å: Chain A: Q.461 Ligands: PG4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.461 NA.10: 2 residues within 4Å: Chain B: Q.461 Ligands: PG4.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiser, P.D. et al., Rational Tuning of Visual Cycle Modulator Pharmacodynamics. J. Pharmacol. Exp. Ther. (2017)

Release Date

2017-05-17

Peptides

Retinoid isomerohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinoid isomerohydrolase

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