SMTL ID : 5eto.1

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.07 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

monomer

Ligands

1 x 5RY: 4-[(2-azanyl-6-oxidanylidene-1,9-dihydropurin-8-yl)sulfanylmethyl]-3-fluoranyl-benzenecarbonitrile(Non-covalent)

5RY.1: 11 residues within 4Å: Chain A: T.46, P.47, P.48, L.49, G.50, Y.57, N.59, W.93, R.125, F.127 Ligands: APC.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.49 Hydrogen bonds: A:T.46, A:P.47, A:L.49, A:L.49, A:G.50, A:N.59, A:N.59 Water bridges: A:R.96, A:R.125 pi-Stacking: A:Y.57, A:Y.57, A:W.93, A:W.93, A:F.127 pi-Cation interactions: A:F.127

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 20 residues within 4Å: Chain A: L.74, Q.78, R.86, R.88, W.93, 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: 5RY.1, CA.3, CA.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.78, A:R.86, A:R.86, A:R.88, A:R.88, A:R.96, A:R.96, A:D.99, A:I.102, A:T.116, A:T.116, A:Y.120 Water bridges: A:R.125 Salt bridges: A:H.119, A:R.125

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.2, CA.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.4: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.2, CA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.3, H2O.5 CA.5: 1 residues within 4Å: Chain A: E.113 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.113, H2O.5, H2O.5 CA.6: 2 residues within 4Å: Chain A: D.53, E.91 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.53, A:E.91, H2O.2, H2O.3, H2O.4

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

CL.7: 5 residues within 4Å: Chain A: G.85, R.86, V.87, R.96, T.97 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: P.118, K.123, F.141, P.142, D.143 Ligand excluded by PLIP

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
A

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

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