SMTL ID : 4wql.1

Crystal structure of aminoglycoside nucleotidylyltransferase ANT(2")-Ia, kanamycin-bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.45, D.47 Ligands: MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.45, A:D.47, H2O.8, H2O.8, H2O.8 MG.2: 5 residues within 4Å: Chain A: D.45, D.47, D.87 Ligands: MG.1, KAN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.45, A:D.45, A:D.47, A:D.87

1 x KAN: KANAMYCIN A(Non-covalent)

KAN.3: 13 residues within 4Å: Chain A: D.45, D.47, Y.75, D.87, E.89, I.100, A.101, D.132, Y.135, E.139 Ligands: MG.2, IPA.7, GOL.13 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.45, A:D.87, A:E.89, A:A.101, A:E.102, A:E.139 Water bridges: A:D.132, A:Y.136

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 3 residues within 4Å: Chain A: G.29, H.43, D.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.44 Water bridges: A:G.29, A:D.45 IPA.5: 3 residues within 4Å: Chain A: P.23, W.93, E.110 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.93, A:E.110 IPA.6: 4 residues within 4Å: Chain A: F.134, P.142, W.145, Y.153 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.134, A:W.145, A:Y.153, A:Y.153 IPA.7: 3 residues within 4Å: Chain A: D.132, Y.133 Ligands: KAN.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.132, A:Y.133 IPA.8: 1 residues within 4Å: Chain A: W.92 No protein-ligand interaction detected (PLIP) IPA.9: 2 residues within 4Å: Chain A: E.96, E.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.96

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: P.104, V.167 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.127 GOL.11: 2 residues within 4Å: Chain A: E.53, W.92 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.52, A:E.53, A:E.53 GOL.12: 3 residues within 4Å: Chain A: E.80, G.82, D.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.83 GOL.13: 8 residues within 4Å: Chain A: G.27, G.28, E.89, I.100, N.124, I.129, D.132 Ligands: KAN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.28, A:D.132, A:D.132 Water bridges: A:L.48, A:D.132, A:D.132, A:D.132, A:D.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cox, G. et al., Structural and Molecular Basis for Resistance to Aminoglycoside Antibiotics by the Adenylyltransferase ANT(2)-Ia. Mbio (2015)

Release Date

2014-11-12

Peptides

2''-aminoglycoside nucleotidyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2''-aminoglycoside nucleotidyltransferase

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