SMTL ID : 4fev.4 (8 other biounits)

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x KAN: KANAMYCIN A(Non-covalent)

KAN.1: 10 residues within 4Å: Chain A: D.166, F.167, D.168, D.199, N.235, C.236, E.239, D.269, E.270, F.272 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.166, A:D.166, A:D.166, A:D.168, A:D.199, A:N.235, A:N.235, A:E.239, A:D.269, A:F.272 Water bridges: A:D.169, A:D.199, A:D.199, A:D.203, A:D.203, A:N.204, A:N.204, A:F.272

1 x PP1: 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE(Non-covalent)

PP1.2: 8 residues within 4Å: Chain A: I.41, F.54, P.83, T.100, A.101, I.102, Q.109, I.216 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.41, A:F.54, A:I.216, A:I.216 Hydrogen bonds: A:I.102, A:I.102 pi-Stacking: A:F.54, A:F.54

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: N.235 No protein-ligand interaction detected (PLIP) NA.4: 4 residues within 4Å: Chain A: T.77, M.80, P.81, L.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.77, A:T.77, A:L.82

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: R.130, R.226, Y.252 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.130 Hydrogen bonds: A:Y.252 Water bridges: A:R.226 Salt bridges: A:R.130, A:R.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance. Biochem.J. (2013)

Release Date

2012-06-20

Peptides

Aminoglycoside 3'-phosphotransferase AphA1-IAB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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