SMTL ID : 5aes.1

Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with a PNP-derived Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 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: 5B0.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.26, A:D.28, A:D.235, H2O.1, H2O.1 MG.3: 7 residues within 4Å: Chain B: D.26, D.28, G.29, V.30, D.235, D.240 Ligands: 5B0.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.26, B:D.28, B:D.235, H2O.1, H2O.2

2 x 5B0: {2-[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]ethyl}phosphonic acid(Non-covalent)

5B0.2: 15 residues within 4Å: Chain A: D.26, C.27, D.28, V.58, S.59, N.60, N.61, S.62, R.63, Y.147, D.176, H.179, T.187, K.210 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:D.26, A:C.27, A:D.28, A:D.28, A:V.58, A:N.60, A:K.210 Water bridges: A:N.60, A:S.62, A:D.176, A:H.179, A:T.239 pi-Stacking: A:H.179 5B0.4: 16 residues within 4Å: Chain B: D.26, C.27, D.28, V.58, S.59, N.60, N.61, S.62, R.63, Y.147, D.176, H.179, T.187, K.210 Ligands: MG.3, GOL.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.147 Hydrogen bonds: B:D.26, B:C.27, B:D.28, B:D.28, B:V.58, B:N.60, B:N.61, B:R.63, B:K.210 Water bridges: B:S.62, B:T.239, B:T.239 pi-Stacking: B:H.179

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain B: D.28, W.32, G.34, N.61, R.63, R.64, R.72, L.181 Ligands: 5B0.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.28, B:D.28, B:W.32, B:N.61, B:R.63, B:R.64, B:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knobloch, G. et al., Synthesis of Hydrolysis-Resistant Pyridoxal 5'-Phosphate Analogs and Their Biochemical and X-Ray Crystallographic Characterization with the Pyridoxal Phosphatase Chronophin. Bioorg.Med.Chem. (2015)

Release Date

2015-04-01

Peptides

PYRIDOXAL PHOSPHATE PHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRIDOXAL PHOSPHATE PHOSPHATASE

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