SMTL ID : 4gkh.18 (17 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: W.234, N.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.235 NA.5: 4 residues within 4Å: Chain A: T.77, M.80, P.81, L.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.77, A:L.82 NA.10: 4 residues within 4Å: Chain B: T.77, M.80, P.81 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.77, B:L.82

2 x KAN: KANAMYCIN A(Non-covalent)

KAN.2: 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 20 PLIP interactions: 20 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:E.239, A:D.269, A:F.272 Water bridges: A:D.169, A:D.199, A:L.202, A:D.203, A:D.203, A:D.203, A:D.203, A:N.204, A:D.217, A:D.217, A:R.220 KAN.8: 12 residues within 4Å: Chain A: S.3, H.4 Chain B: D.166, F.167, D.168, D.199, N.235, C.236, E.239, D.269, E.270, F.272 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:S.3, B:D.166, B:F.167, B:D.199, B:D.203, B:N.235, B:E.239, B:D.269, B:F.272 Water bridges: B:S.37, B:D.168, B:D.168, B:D.169, B:D.203, B:D.203, B:N.204, B:N.204, B:N.204, B:N.235

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

ACT.3: 7 residues within 4Å: Chain A: G.38, A.39, T.40, H.57, G.58, K.59, V.62 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.59 Hydrogen bonds: A:T.40, A:K.59 ACT.6: 5 residues within 4Å: Chain A: W.234, M.259, L.262, Q.263, L.266 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.234 ACT.7: 5 residues within 4Å: Chain A: V.110, Y.114, S.117, I.121, G.210 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.121 Water bridges: A:G.210 ACT.11: 3 residues within 4Å: Chain B: D.21, A.22, Y.25 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.25 ACT.12: 6 residues within 4Å: Chain B: T.77, A.78, F.79, M.80, P.81 Ligands: NA.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.79 Water bridges: B:L.82, B:R.131 ACT.13: 2 residues within 4Å: Chain B: Y.114, S.117 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.117, B:S.117 Water bridges: B:G.210 ACT.14: 3 residues within 4Å: Chain B: M.259, L.262, Q.263 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.262, B:Q.263 Water bridges: B:E.170 ACT.15: 7 residues within 4Å: Chain A: Q.6 Chain B: V.34, T.106, D.203, N.204, I.216 Ligands: 0J9.9 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.6 Water bridges: A:I.5, B:D.203 Hydrophobic interactions: B:V.34, B:D.203

2 x 0J9: 1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

0J9.4: 7 residues within 4Å: Chain A: D.32, F.54, P.83, T.100, A.101, I.102, I.216 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.54, A:F.54 Hydrogen bonds: A:I.102, A:I.102 0J9.9: 14 residues within 4Å: Chain A: Q.6 Chain B: D.32, V.34, I.41, F.54, P.83, A.101, I.102, T.106, Q.109, I.206, I.216, D.217 Ligands: ACT.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.34, B:I.41, B:F.54, B:F.54, B:T.106, B:I.206, B:I.216, B:I.216 Hydrogen bonds: B:I.102, B:I.102 pi-Stacking: B:F.54, B:F.54

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
K

B
L

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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