SMTL ID : 8s8a.1

Human pyridoxal phosphatase in complex with 7,8-dihydroxyflavone without phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x UK9: 7,8-bis(oxidanyl)-2-phenyl-chromen-4-one(Non-covalent)

UK9.1: 17 residues within 4Å: Chain A: D.27, G.28, N.32, G.33, N.60, R.62, Y.150, H.182, P.183, L.184, T.190, D.238, R.239, G.260, V.261 Ligands: FMT.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.27, A:H.182, A:P.183, A:T.190, A:V.261 Hydrogen bonds: A:G.33, A:H.182, A:R.239 Water bridges: A:D.27, A:D.27, A:D.27, A:D.27, A:D.238 pi-Stacking: A:Y.150, A:H.182 UK9.5: 17 residues within 4Å: Chain B: D.27, G.28, N.32, G.33, N.60, R.62, Y.150, H.182, P.183, L.184, T.190, D.238, R.239, G.260, V.261 Ligands: FMT.6, MG.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:D.27, B:H.182, B:P.183, B:T.190, B:V.261 Hydrogen bonds: B:G.33, B:H.182, B:R.239 Water bridges: B:D.27, B:D.238, B:D.238 pi-Stacking: B:Y.150, B:H.182

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: N.60, R.62, R.63 Ligands: UK9.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.60, A:R.62, A:R.63, A:R.63 Water bridges: A:R.71 FMT.6: 4 residues within 4Å: Chain B: N.60, R.62, R.63 Ligands: UK9.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.60, B:R.62, B:R.63, B:R.63 Water bridges: B:R.71

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.25, D.27, G.28, V.29, D.238 Ligands: UK9.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.25, A:D.27, A:D.238, H2O.1, H2O.1 MG.7: 6 residues within 4Å: Chain B: D.25, D.27, G.28, V.29, D.238 Ligands: UK9.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.25, B:D.27, B:D.238, H2O.12, H2O.12

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: V.110, F.111, V.112, R.119, L.129, A.130 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: V.110, F.111, V.112, R.119, L.129, A.130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brenner, M. et al., 7,8-Dihydroxyflavone is a direct inhibitor of human and murine pyridoxal phosphatase. Elife (2024)

Release Date

2024-06-12

Peptides

Chronophin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Chronophin

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