SMTL ID : 7q10.1

Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: D.93, T.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.96, A:T.96 GOL.2: 3 residues within 4Å: Chain A: Y.144, Y.180, Y.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.210 GOL.4: 5 residues within 4Å: Chain A: L.86, P.193, W.204, V.205, T.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.205, A:T.206 GOL.8: 8 residues within 4Å: Chain B: D.170, H.176, T.212, G.213, D.214, P.215, S.220, F.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.170, B:D.214, B:F.221 GOL.9: 5 residues within 4Å: Chain B: V.148, E.149, S.150, A.153, K.154 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.149, B:S.150, B:S.150, B:K.154 Water bridges: B:E.149, B:E.149 GOL.10: 4 residues within 4Å: Chain B: I.70, D.72, E.123 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.123 Water bridges: B:W.67, B:D.72, B:D.72, B:E.123 GOL.12: 10 residues within 4Å: Chain B: D.72, E.123, V.190, Y.192, D.209, Y.210, D.211, T.212, G.213 Ligands: GOL.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.72, B:D.72, B:D.209, B:D.211, B:D.211, B:T.212, B:G.213 Water bridges: B:E.123

1 x 8I5: 3N methyl nemycin B(Non-covalent)

8I5.3: 9 residues within 4Å: Chain A: D.72, E.123, D.211, T.212, G.213, D.214, P.215 Chain B: P.215, D.218 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.123, A:D.211, A:T.212, A:D.214, A:D.214, B:D.218, B:D.218 Water bridges: A:D.211, A:T.212, A:G.213

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: D.170, T.171, H.176, T.212 Chain B: D.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.176 PEG.11: 5 residues within 4Å: Chain B: H.117, R.118, A.134, T.137, A.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.118, B:A.134

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: Y.180, L.181, Y.210 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.180 Hydrogen bonds: A:Y.210 Salt bridges: A:K.187

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

CL.7: 6 residues within 4Å: Chain A: A.32, S.33, V.34, N.103, S.104, V.105 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: A.32, S.33, V.34, N.103, S.104, V.105 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pontillo, N. et al., 3-N-alkylation in aminoglycoside antibiotic neomycin B overcomes bacterial resistance mediated by acetyltransferase (3) IIIa. To Be Published

Release Date

2022-11-02

Peptides

Aminoglycoside N(3)-acetyltransferase III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminoglycoside N(3)-acetyltransferase III

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