SMTL ID : 7uuj.1

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with gentamicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-trimer

Ligands

3 x LLL: (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL(Non-covalent)

LLL.1: 9 residues within 4Å: Chain A: D.57, D.83, E.87, Y.104 Chain C: N.115, H.137, D.146, D.147, Y.172 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:E.87, A:Y.104, C:N.115, C:D.147 Water bridges: A:Y.186, C:N.115, C:N.115, C:D.146 Hydrophobic interactions: C:Y.172, C:Y.172 LLL.4: 10 residues within 4Å: Chain A: N.115, H.137, D.146, D.147, Y.172 Chain B: D.57, D.83, E.87, Y.104, G.129 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.57, B:D.57, B:D.57, B:E.87, B:Y.104, A:N.115, A:D.147 Water bridges: B:G.129, B:Y.186, B:Y.186 Hydrophobic interactions: A:Y.172 LLL.6: 9 residues within 4Å: Chain B: H.137, D.146, D.147, Y.172 Chain C: D.57, D.83, E.87, Y.104, G.129 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Y.172 Hydrogen bonds: B:D.147, C:D.57, C:E.87, C:Y.104, C:Y.104 Water bridges: B:N.115, B:N.115, C:G.129

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

EDO.2: 5 residues within 4Å: Chain A: Q.149, Q.161, L.164, Y.172, Y.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.149, A:Q.161, A:Q.161 EDO.5: 5 residues within 4Å: Chain B: W.251, E.255, N.259, K.272, Y.273 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.255, B:N.259, B:K.272, B:K.272 EDO.8: 2 residues within 4Å: Chain A: V.224 Chain C: L.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.209 EDO.10: 1 residues within 4Å: Chain C: E.154 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: E.254 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.254, H2O.11, H2O.18, H2O.20

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

CL.9: 1 residues within 4Å: Chain C: D.57 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J., Crystal structure of aminoglycoside resistance enzyme ApmA, complex with gentamicin. To Be Published

Release Date

2023-04-19

Peptides

Aminocyclitol acetyltransferase ApmA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Aminocyclitol acetyltransferase ApmA

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