SMTL ID : 9em1.1

Human pyridoxal phosphatase in complex with 7,8-dihydroxyflavone and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.25, D.27, V.29, D.238 Ligands: PO4.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.25, A:D.27, A:D.238, H2O.2, H2O.2 MG.6: 5 residues within 4Å: Chain B: D.25, D.27, V.29, D.238 Ligands: PO4.9 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.13

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

UK9.2: 12 residues within 4Å: Chain A: D.27, N.60, S.61, R.62, G.115, Y.150, E.152, H.182, P.183, L.184, T.190 Ligands: GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.62, A:Y.150, A:H.182 Hydrogen bonds: A:S.61, A:S.61, A:R.62, A:E.152 Water bridges: A:R.62, A:T.193 pi-Stacking: A:Y.150, A:Y.150 UK9.7: 12 residues within 4Å: Chain B: D.27, N.60, S.61, R.62, G.115, Y.150, E.152, H.182, P.183, L.184, T.190 Ligands: GOL.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.62, B:Y.150, B:H.182 Hydrogen bonds: B:S.61, B:S.61, B:R.62, B:E.152 Water bridges: B:R.62, B:E.152, B:T.193 pi-Stacking: B:Y.150, B:Y.150

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: D.27, W.31, G.33, E.34, N.60, R.62, R.63, R.71 Ligands: UK9.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.27, A:W.31, A:G.33, A:E.34, A:N.60, A:R.62, A:R.63, A:R.63, A:R.71 GOL.8: 9 residues within 4Å: Chain B: D.27, W.31, G.33, E.34, N.60, R.62, R.63, R.71 Ligands: UK9.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.27, B:W.31, B:G.33, B:E.34, B:N.60, B:R.62, B:R.63, B:R.63, B:R.71

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 8 residues within 4Å: Chain A: D.25, C.26, D.27, S.58, N.59, N.60, K.213 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:C.26, A:D.27, A:D.27, A:S.58, A:S.58, A:S.58, A:N.59, A:N.60 Water bridges: A:N.59, A:H.182, A:K.213, A:K.213, A:K.213, A:R.239 Salt bridges: A:K.213 PO4.5: 6 residues within 4Å: Chain A: R.65, E.83, F.86, R.94, N.225, F.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.225 Salt bridges: A:R.65, A:R.94 PO4.9: 8 residues within 4Å: Chain B: D.25, C.26, D.27, S.58, N.59, N.60, K.213 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:C.26, B:D.27, B:S.58, B:S.58, B:S.58, B:N.59, B:N.60 Water bridges: B:N.59, B:D.179, B:H.182, B:K.213, B:K.213, B:K.213, B:R.239 Salt bridges: B:K.213 PO4.10: 6 residues within 4Å: Chain B: R.65, E.83, F.86, R.94, N.225, F.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.225 Salt bridges: B:R.65, B:R.94

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

Related Entries With Identical Sequence