SMTL ID : 5cft.1

Crystal Structure of ANT(2")-Ia in complex with AMPCPP and gentamicin C1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.52, D.54 Ligands: MN.2, APC.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:D.54, H2O.2 MN.2: 6 residues within 4Å: Chain A: D.52, D.54, D.94 Ligands: MN.1, APC.3, 51G.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.52, A:D.54, A:D.94

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 14 residues within 4Å: Chain A: G.35, G.36, R.48, H.50, D.51, D.52, D.54, D.139, Y.140, Y.143, H.156 Ligands: MN.1, MN.2, 51G.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.36, A:R.48, A:D.51, A:D.52, A:Y.140 Water bridges: A:W.37, A:W.37, A:Y.143, A:S.159 Salt bridges: A:R.48, A:H.50 pi-Stacking: A:Y.143, A:Y.143

1 x 51G: gentamicin C1(Non-covalent)

51G.4: 12 residues within 4Å: Chain A: D.52, D.54, Y.82, L.85, D.94, E.96, I.107, A.108, D.139, Y.142 Ligands: MN.2, APC.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.142 Hydrogen bonds: A:D.94, A:E.96, A:E.96 Water bridges: A:D.139, A:Y.143

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 5 residues within 4Å: Chain A: T.15, L.16, K.19, L.72, I.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bassenden, A.V. et al., Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design. Acs Chem.Biol. (2016)

Release Date

2016-03-16

Peptides

Aminoglycoside Nucleotidyltransferase (2")-Ia: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminoglycoside Nucleotidyltransferase (2")-Ia

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