SMTL ID : 4dfu.2 (1 other biounit)

Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA in complex with kanamycin inhibited with quercetin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

2 x QUE: 3,5,7,3',4'-PENTAHYDROXYFLAVONE(Non-covalent)

QUE.1: 8 residues within 4Å: Chain A: S.72, R.73, T.76, S.106, E.107, T.108, Y.109, Q.110 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.76, A:Q.110 Hydrogen bonds: A:S.106 QUE.3: 13 residues within 4Å: Chain A: I.65, K.67, E.81, P.97, F.116, T.117, K.118, I.119, G.121, P.123, L.225, I.237, D.238 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.65, A:I.65, A:P.97, A:F.116, A:I.237 Hydrogen bonds: A:E.81, A:I.119, A:I.119

1 x KAN: KANAMYCIN A(Non-covalent)

KAN.2: 12 residues within 4Å: Chain A: D.218, S.220, D.222, H.223, D.241, E.256, E.259, E.260, E.289, W.292, Y.299, W.308 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.218, A:S.220, A:D.241, A:D.241, A:E.259, A:E.260, A:E.289 Water bridges: A:D.241, A:Y.299, A:Y.299

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

CL.4: 3 residues within 4Å: Chain A: K.134, N.138, K.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shakya, T. et al., A small molecule discrimination map of the antibiotic resistance kinome. Chem.Biol. (2011)

Release Date

2012-02-08

Peptides

APH(2")-Id: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

APH(2")-Id

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