SMTL ID : 5etl.3 (3 other biounits)

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.82 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: CA.2, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.1, H2O.4 CA.2: 5 residues within 4Å: Chain A: D.99, D.101, R.125 Ligands: CA.1, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.4, H2O.5 CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 18 residues within 4Å: Chain A: L.74, Q.78, R.86, R.88, R.96, D.99, L.100, D.101, I.102, R.114, L.115, T.116, V.117, H.119, Y.120, R.125 Ligands: CA.1, CA.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.78, A:D.99, A:I.102, A:T.116, A:T.116, A:Y.120, A:Y.120 Water bridges: A:R.86, A:R.86, A:R.96, A:R.96, A:T.116, A:R.125 Salt bridges: A:R.86, A:R.88, A:R.96, A:H.119, A:R.125

1 x 5RV: 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile(Non-covalent)

5RV.5: 10 residues within 4Å: Chain A: T.46, P.47, P.48, L.49, G.50, Y.57, N.59, R.96, R.125, F.127 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.49, A:F.127 Hydrogen bonds: A:T.46, A:T.46, A:P.47, A:L.49, A:L.49, A:N.59 Water bridges: A:R.96, A:R.96, A:R.125 pi-Stacking: A:Y.57, A:F.127 pi-Cation interactions: A:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dennis, M.L. et al., Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. J.Med.Chem. (2016)

Release Date

2016-05-04

Peptides

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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