SMTL ID : 4gki.15 (17 other biounits)

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NM-PP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x KAN: KANAMYCIN A(Non-covalent)

KAN.1: 12 residues within 4Å: Chain A: Q.36, D.166, F.167, D.168, D.199, R.220, N.235, C.236, E.239, D.269, E.270, F.272 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.166, A:D.166, A:F.167, A:D.168, A:D.199, A:D.199, A:R.220, A:R.220, A:N.235, A:E.239, A:E.239, A:D.269, A:F.272 Water bridges: A:Q.36, A:R.156, A:D.203, A:D.203, A:D.203, A:N.204, A:N.204, A:C.236, B:H.4 KAN.9: 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.166, B:F.167, B:D.168, B:D.199, B:D.199, B:N.235, B:E.239, B:E.239, B:D.269, B:F.272 Water bridges: B:D.169, B:D.203, B:D.203, B:N.204, B:N.204, B:N.204

2 x 0JN: 1-tert-butyl-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

0JN.2: 14 residues within 4Å: Chain A: D.32, I.41, R.43, F.54, P.83, T.100, A.101, I.102, G.104, I.206, I.216, D.217 Chain B: Q.6, E.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.41, A:F.54, A:F.54, A:F.54 Hydrogen bonds: A:I.102, A:I.102 pi-Stacking: A:F.54 0JN.10: 12 residues within 4Å: Chain A: R.7 Chain B: D.32, I.41, F.54, P.83, T.100, A.101, I.102, G.104, I.206, I.216, D.217 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.41, B:F.54, B:F.54, B:F.54, B:F.54 Hydrogen bonds: B:I.102, B:I.102

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

NA.3: 4 residues within 4Å: Chain A: T.77, M.80, P.81 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.77, A:L.82 Water bridges: A:T.77 NA.11: 4 residues within 4Å: Chain B: T.77, M.80, P.81, L.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.82 Water bridges: B:T.77, B:T.77

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

ACT.4: 4 residues within 4Å: Chain A: D.169, E.170, N.172, W.174 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.170 ACT.5: 4 residues within 4Å: Chain A: W.234, M.259, L.262, L.266 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.234, A:L.262, A:L.266 ACT.6: 2 residues within 4Å: Chain A: R.31, T.40 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.40 Salt bridges: A:R.31 ACT.7: 6 residues within 4Å: Chain A: T.77, A.78, F.79, M.80, P.81 Ligands: NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.79 Water bridges: A:L.82, A:R.131 ACT.8: 4 residues within 4Å: Chain A: V.110, S.117, I.121, G.210 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.121 Hydrogen bonds: A:S.117 Water bridges: A:G.210 ACT.12: 6 residues within 4Å: Chain B: G.38, T.40, H.57, G.58, K.59, V.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.40, B:T.40, B:K.59

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

2012-09-05

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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