SMTL ID : 7uun.1

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with neomycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-trimer

Ligands

3 x NMY: NEOMYCIN(Non-covalent)

NMY.1: 11 residues within 4Å: Chain A: E.114, N.115, H.134, H.137, D.146, D.147 Chain B: E.87, Y.104, N.128, G.129 Ligands: EDO.2 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.104, B:Y.104, B:N.128, B:N.128, B:G.129, A:N.115, A:H.137, A:D.146, A:D.146 Water bridges: B:D.83, B:E.87 NMY.3: 11 residues within 4Å: Chain B: E.114, N.115, H.134, H.137, D.146, D.147 Chain C: E.87, Y.104, N.128, G.129 Ligands: EDO.4 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Y.104, C:N.128, C:N.128, C:G.129, B:N.115, B:H.137, B:D.146, B:D.146 Water bridges: C:D.83, C:E.87 NMY.5: 11 residues within 4Å: Chain A: E.87, Y.104, N.128, G.129 Chain C: E.114, N.115, H.134, H.137, D.146, D.147 Ligands: EDO.6 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:N.115, C:H.137, C:D.146, A:Y.104, A:Y.104, A:N.128, A:N.128, A:G.129 Water bridges: A:D.83, A:E.87

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: D.147 Chain B: E.87 Ligands: NMY.1 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain B: D.147 Chain C: E.87 Ligands: NMY.3 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: E.87 Chain C: D.147 Ligands: NMY.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bordeleau, E. et al., Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat.Chem.Biol. (2024)

Release Date

2022-11-02

Peptides

Aminocyclitol acetyltransferase ApmA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Aminocyclitol acetyltransferase ApmA

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