SMTL ID : 4gkh.14 (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

2 x KAN: KANAMYCIN A(Non-covalent)

KAN.1: 13 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 Chain B: H.4 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.36, A:D.166, A:D.166, A:F.167, A:D.168, A:D.199, A:R.220, A:R.220, A:N.235, A:N.235, A:E.239, A:D.269, A:F.272, B:H.4 Water bridges: A:R.156, A:R.156, A:D.169, A:D.203, A:D.203, A:N.204, A:N.204 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:D.166, B:F.167, B:D.168, B:D.199, B:N.235, B:E.239, B:D.269, B:F.272 Water bridges: B:D.169, B:D.199, B:S.201, B:D.203, B:D.203, B:D.203, B:N.204, B:N.204, B:N.204, B:E.239

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

0J9.2: 13 residues within 4Å: Chain A: D.32, N.33, F.54, P.83, T.100, A.101, I.102, T.106, Q.109, I.206, I.216, D.217 Chain B: Q.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.54, A:F.54, A:F.54, A:T.106, A:I.206, A:I.216 Hydrogen bonds: A:I.102, A:I.102 pi-Stacking: A:F.54, A:F.54 0J9.3: 14 residues within 4Å: Chain A: Q.6 Chain B: D.32, I.41, F.54, P.83, T.100, A.101, I.102, G.104, T.106, Q.109, I.206, I.216, D.217 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.41, B:F.54, B:F.54, B:F.54, B:T.106, B:I.206 Hydrogen bonds: B:I.102, B:I.102

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

NA.4: 5 residues within 4Å: Chain A: T.77, M.80, P.81, L.82 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.77, A:L.82 Water bridges: A:T.77

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: Q.36, S.37, G.38, A.39 Ligand excluded by PLIP

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

ACT.6: 3 residues within 4Å: Chain A: 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.7: 6 residues within 4Å: Chain A: T.77, A.78, F.79, M.80, P.81 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.79 Water bridges: A:L.82, A:R.131 ACT.8: 2 residues within 4Å: Chain A: R.31, T.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.40 Salt bridges: A:R.31 ACT.10: 6 residues within 4Å: Chain B: T.77, A.78, F.79, M.80, P.81, R.131 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.131 ACT.12: 7 residues within 4Å: Chain B: G.38, A.39, 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 ACT.13: 3 residues within 4Å: Chain B: P.188, F.189, S.190 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.146 ACT.14: 4 residues within 4Å: Chain B: F.108, E.112, E.239, F.240 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.240 Hydrogen bonds: B:E.112

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

PEG.11: 4 residues within 4Å: Chain B: Y.114, S.117, N.120, G.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.117, B:N.120 PEG.15: 5 residues within 4Å: Chain B: R.130, S.134, R.226, Y.252, I.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.134 Water bridges: B:D.192, B:D.192, B: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

2012-09-05

Peptides

Aminoglycoside 3'-phosphotransferase AphA1-IAB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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