SMTL ID : 8qfw.1

Murine pyridoxal phosphatase in complex with 7,8-dihydroxyflavone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.26, D.28, G.29, V.30, D.235, D.240 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.26, A:D.28, A:D.235, H2O.2, H2O.2 MG.7: 8 residues within 4Å: Chain B: D.26, D.28, G.29, V.30, D.235, R.236, D.240 Ligands: PO4.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.26, B:D.28, B:D.235, H2O.9, H2O.9

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

PO4.2: 9 residues within 4Å: Chain A: D.26, C.27, D.28, S.59, N.60, N.61, K.210 Ligands: MG.1, UK9.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:C.27, A:D.28, A:S.59, A:S.59, A:N.60, A:N.61 Water bridges: A:N.60, A:H.179, A:K.210, A:K.210, A:R.236, A:T.239 Salt bridges: A:K.210 PO4.8: 8 residues within 4Å: Chain B: D.26, C.27, D.28, S.59, N.60, N.61, K.210 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:C.27, B:D.28, B:S.59, B:S.59, B:N.60, B:N.61 Water bridges: B:N.60, B:K.210, B:K.210, B:T.239 Salt bridges: B:K.210

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

UK9.3: 14 residues within 4Å: Chain A: D.28, N.60, N.61, S.62, R.63, G.116, Y.147, E.149, H.179, P.180, L.181, T.187 Ligands: PO4.2, CIT.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.61, A:R.63, A:Y.147, A:H.179, A:L.181 Hydrogen bonds: A:N.61, A:S.62, A:S.62, A:R.63, A:E.149 Water bridges: A:S.89 pi-Stacking: A:Y.147, A:Y.147

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

PGE.4: 7 residues within 4Å: Chain A: N.54, T.55, L.56, Q.85, F.223, S.224, V.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.55, A:S.224, A:S.224

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 9 residues within 4Å: Chain A: D.28, G.34, N.61, R.63, R.64, R.72, L.181, S.182 Ligands: UK9.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.181 Hydrogen bonds: A:D.28, A:G.34, A:N.61, A:R.63, A:S.182, A:S.182 Salt bridges: A:R.63, A:R.63, A:R.64, A:R.72

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: R.139, V.140, A.161, H.162, D.165, C.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.140, A:D.165 GOL.9: 9 residues within 4Å: Chain B: D.28, W.32, G.34, N.61, R.63, R.64, R.72, P.180, L.181 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.28, B:N.61, B:R.63, B:R.63, B:R.64, B:R.64 Water bridges: B:W.32

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
B

Chronophin