SMTL ID : 5iqd.1 (3 other biounits)

Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPNP, Magnesium, and Ribostamycin

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: 16 residues within 4Å: Chain A: I.34, 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: MG.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.40, A:K.52, A:K.52, A:I.103, A:I.103, A:I.103 Water bridges: A:G.37, A:G.37, A:Y.63, A:Y.100, A:G.105, A:N.204, A:N.204, A:H.205, A:D.222, A:D.222 Salt bridges: A:K.52, A:E.102

1 x RIO: RIBOSTAMYCIN(Non-covalent)

RIO.2: 11 residues within 4Å: Chain A: D.200, S.202, Y.234, E.237, S.239, E.241, E.242, V.270, E.271, Y.274, E.277 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.200, A:S.202, A:E.237, A:E.241, A:E.241, A:E.241, A:E.271 Water bridges: A:N.204, A:Y.234, A:Y.234, A:Y.234, A:E.237, A:E.240, A:Q.267, 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 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., Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia. Structure (2016)

Release Date

2016-05-25

Peptides

Bifunctional AAC/APH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional AAC/APH

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