SMTL ID : 6cgd.1 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

GNP.1: 19 residues within 4Å: Chain A: I.34, S.36, G.37, S.40, A.42, I.50, K.52, Y.63, Y.100, E.102, I.103, F.107, H.205, L.207, I.218, D.219 Ligands: AKN.2, MG.3, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.36, A:S.40, A:K.52, A:I.103, A:I.103, A:I.103, A:D.219 Water bridges: A:S.36, A:S.36, A:G.37, A:G.37, A:Y.38, A:S.40, A:Y.63, A:E.66, A:Y.100, A:G.105, A:N.204, A:N.204, A:N.204, A:H.205, A:D.219, A:G.221 Salt bridges: A:K.52, A:E.102

1 x AKN: (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide(Non-covalent)

AKN.2: 12 residues within 4Å: Chain A: S.36, G.37, Y.38, D.200, D.222, Y.234, E.237, V.270, E.271, Y.274, E.277 Ligands: GNP.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.38, A:Y.38, A:D.222, A:D.222, A:Y.234, A:E.237, A:E.277, A:E.277 Water bridges: A:S.36, A:N.204, A:N.204, A:D.219, A:D.219, A:E.237, A:E.237, A:Q.267

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.205, D.219 Ligands: GNP.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.205, A:D.219, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.219 Ligands: GNP.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.219, A:D.219, H2O.1, H2O.1, H2O.1

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

CL.5: 4 residues within 4Å: Chain A: Q.288, I.291, E.292, R.295 Ligand excluded by PLIP

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
A

Bifunctional AAC/APH

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