SMTL ID : 6cey.4 (3 other biounits)

Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Lividomycin moieties

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 16 residues within 4Å: Chain A: I.34, S.40, A.42, I.50, K.52, Y.100, E.102, I.103, F.107, D.200, H.205, I.218, D.219 Ligands: LIV.2, MG.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.40, A:K.52, A:Y.100, A:I.103, A:I.103, A:I.103, A:D.200, A:D.219, A:D.219 Water bridges: A:K.52, A:E.66, A:N.204, A:N.204, A:D.219, A:D.219, A:D.219 Salt bridges: A:K.52, A:E.102

1 x LIV: (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL(Non-covalent)

LIV.2: 12 residues within 4Å: Chain A: D.200, S.202, N.204, D.222, Y.234, E.237, S.239, E.241, E.242, Y.274, E.277 Ligands: GNP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.200, A:D.200, A:S.202, A:N.204, A:E.237, A:E.237, A:E.241, A:E.242, A:Y.274, A:Y.274 Water bridges: A:E.277, A:E.277

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.205, D.219 Ligands: GNP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.205, A:D.219, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.219 Ligands: GNP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.219, A:D.219, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caldwell, S.J. et al., Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2′′)-Ia. Antimicrob. Agents Chemother. (2018)

Release Date

2018-04-11

Peptides

Bifunctional AAC/APH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Bifunctional AAC/APH

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