SMTL ID : 6mn5.1 (5 other biounits)

Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, H154A mutant, in complex with gentamicin C1A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

1 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: 10 residues within 4Å: Chain A: G.69, D.71, Y.187, E.189, D.191, H.192, C.193, C.194, E.253 Ligands: EDO.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.71, A:Y.187, A:E.189, A:E.189, A:H.192, A:E.253 Water bridges: A:D.152, A:D.152

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.193, H.245, C.251, C.254 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.193, A:H.245, A:C.251, A:C.254

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: E.8, F.35, R.39, P.40, L.41, E.42, G.44 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.41, A:G.44 Water bridges: A:D.43 Salt bridges: A:E.8, A:E.8, A:R.39 EPE.4: 7 residues within 4Å: Chain A: S.34, F.35, R.36, D.85, G.87, V.88 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.35, A:R.36, A:D.85, A:V.88 Salt bridges: A:D.85

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: P.84, V.88, D.91 Ligands: EPE.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.84, A:D.91, A:D.91

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

EDO.6: 1 residues within 4Å: Chain A: R.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.95 EDO.7: 2 residues within 4Å: Chain A: S.208, Q.210 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: D.43, G.44, P.45, L.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43, A:L.46 EDO.9: 2 residues within 4Å: Chain A: E.42, D.43 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.43, A:E.50 EDO.10: 3 residues within 4Å: Chain A: P.77, K.100, R.101 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.116 EDO.11: 4 residues within 4Å: Chain A: W.67, F.106, H.128 Ligands: LLL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.128 EDO.12: 1 residues within 4Å: Chain A: S.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.120 EDO.13: 2 residues within 4Å: Chain A: R.224, D.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.224, A:R.224 EDO.14: 5 residues within 4Å: Chain A: R.196, D.239, L.241, L.244, R.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.245, A:R.258, A:R.258 EDO.15: 5 residues within 4Å: Chain A: L.123, P.124, L.125, S.129, P.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.125, A:S.129, A:S.129 EDO.16: 5 residues within 4Å: Chain A: Q.143, L.209, K.211, L.222, R.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.143, A:L.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family. Commun Biol (2022)

Release Date

2018-10-24

Peptides

Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa

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