SMTL ID : 4gki.16 (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: 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 22 PLIP interactions: 22 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:D.199, A:L.202, A:D.203, A:D.203, A:D.203, A:D.203, A:D.203, A:N.204, A:D.217, A:D.217, A:D.217 KAN.7: 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 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.166, B:F.167, B:D.199, B:N.235, B:E.239, B:D.269, B:F.272, A:S.3 Water bridges: B:S.37, B:S.37, B:D.168, B:D.169, B:S.201, B:D.203, B:D.203, B:D.217, B:R.220, B:N.235, B:N.235, B:N.235, A:H.4

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

0JN.2: 8 residues within 4Å: Chain A: D.32, R.43, F.54, P.83, T.100, A.101, I.102, I.216 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.54, A:F.54, A:F.54, A:I.216 Hydrogen bonds: A:I.102, A:I.102 0JN.8: 11 residues within 4Å: Chain A: Q.6 Chain B: D.32, I.41, R.43, F.54, P.83, A.101, I.102, G.104, I.206, I.216 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

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

NA.3: 3 residues within 4Å: Chain A: T.77, M.80, P.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.77, A:L.82 NA.4: 1 residues within 4Å: Chain A: N.235 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.170, A:N.235 NA.9: 3 residues within 4Å: Chain B: T.77, M.80 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.77, B:L.82

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

ACT.5: 5 residues within 4Å: Chain A: W.234, M.259, L.262, Q.263, L.266 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.234, A:L.266 ACT.6: 5 residues within 4Å: Chain A: V.110, Y.114, S.117, I.121, G.210 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.110, A:Y.114 Hydrogen bonds: A:S.117, A:G.210 ACT.10: 6 residues within 4Å: Chain B: T.77, A.78, F.79, M.80, P.81 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.79 Water bridges: B:L.82, B:R.131 ACT.11: 5 residues within 4Å: Chain B: W.234, M.259, L.262, Q.263, L.266 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.263 ACT.12: 4 residues within 4Å: Chain B: V.110, Y.114, S.117, G.210 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.114 Hydrogen bonds: B:S.117, B:S.117 Water bridges: B:G.210

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
G

B
H

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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