SMTL ID : 5etv.1

S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.72 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

APC.1: 18 residues within 4Å: Chain A: L.74, L.78, R.86, R.91, R.95, D.98, V.99, D.100, I.101, K.113, L.114, S.115, V.116, H.118, R.120, R.124 Ligands: MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.86, A:R.86, A:R.91, A:R.95, A:R.95, A:I.101, A:I.101, A:S.115 Water bridges: A:R.91, A:R.91, A:D.98, A:V.99, A:R.120, A:R.120, A:R.124 Salt bridges: A:R.91, A:H.118, A:R.120, A:R.124

1 x 5RZ: 2-azanyl-8-[2-(4-bromophenyl)-2-oxidanylidene-ethyl]sulfanyl-1,9-dihydropurin-6-one(Non-covalent)

5RZ.2: 10 residues within 4Å: Chain A: T.46, A.47, P.48, V.49, G.50, F.57, N.59, R.91, R.124, F.126 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.49 Hydrogen bonds: A:T.46, A:A.47, A:V.49, A:V.49, A:N.59, A:N.59 Water bridges: A:A.47, A:R.95, A:R.124 pi-Stacking: A:F.57, A:F.126 pi-Cation interactions: A:F.57, A:F.126

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.98, D.100 Ligands: APC.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.100, H2O.1, H2O.3 MG.4: 4 residues within 4Å: Chain A: D.98, D.100 Ligands: APC.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.100, H2O.1, H2O.1

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 8 residues within 4Å: Chain A: I.15, H.85, R.86, I.87, R.88, P.94, R.95, T.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.85, A:I.87, A:R.88, A:R.88, A:T.96

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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