SMTL ID : 4few.9 (8 other biounits)

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x KAN: KANAMYCIN A(Non-covalent)

KAN.1: 13 residues within 4Å: Chain A: S.37, D.166, F.167, D.168, D.199, N.235, C.236, E.239, D.269, E.270, F.272 Chain B: S.3, H.4 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.166, A:D.166, A:D.166, A:D.199, A:N.235, A:E.239, A:D.269, A:F.272, B:S.3 Water bridges: A:S.37, A:S.37, A:D.169, A:D.203, A:D.203, A:N.204, A:N.235, A:N.235, B:H.4 KAN.5: 10 residues within 4Å: Chain B: D.166, F.167, D.168, D.199, N.235, C.236, E.239, D.269, E.270, F.272 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.166, B:D.166, B:D.168, B:D.199, B:D.199, B:N.235, B:N.235, B:E.239, B:D.269, B:F.272 Water bridges: B:D.169, B:D.203, B:D.203, B:D.203, B:N.204, B:D.217, B:R.220

2 x PP2: 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE(Non-covalent)

PP2.2: 9 residues within 4Å: Chain A: I.41, F.54, P.83, A.101, I.102, T.106, Q.109, I.216 Chain B: Q.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.41, A:F.54, A:T.106, A:I.216 Hydrogen bonds: A:I.102, A:I.102 Water bridges: A:T.99 pi-Stacking: A:F.54, A:F.54 Halogen bonds: A:Q.109 PP2.6: 9 residues within 4Å: Chain B: I.41, F.54, P.83, T.100, A.101, I.102, T.106, Q.109, I.216 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.41, B:F.54, B:I.216, B:I.216 Hydrogen bonds: B:I.102, B:I.102 pi-Stacking: B:F.54, B:F.54 Halogen bonds: B:Q.109

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

NA.3: 5 residues within 4Å: Chain A: T.77, M.80, P.81, L.82 Ligands: ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.77, A:L.82 NA.7: 2 residues within 4Å: Chain B: W.234, N.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.235 Water bridges: B:D.168 NA.8: 4 residues within 4Å: Chain B: T.77, M.80, P.81 Ligands: ACT.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.82

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

ACT.4: 6 residues within 4Å: Chain A: T.77, A.78, F.79, M.80, P.81 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.79 Water bridges: A:L.82 ACT.9: 6 residues within 4Å: Chain B: T.77, A.78, F.79, M.80, P.81 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.77 Water bridges: B:L.82, B:R.131

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 7 residues within 4Å: Chain B: V.110, Y.114, S.117, N.120, I.121, F.207, G.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.117, B:N.120

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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