SMTL ID : 7ehf.1

Crystal structure of the aminoglycoside resistance methyltransferase NpmB1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: D.31, L.32, G.33, T.103, V.104, N.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.105, A:N.105, A:N.105

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

CL.2: 4 residues within 4Å: Chain A: F.39, T.196, W.197, R.200 Ligand excluded by PLIP

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

EDO.3: 3 residues within 4Å: Chain A: R.15, S.93, E.94 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: Y.25, P.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.48 EDO.5: 5 residues within 4Å: Chain A: D.100, K.131, P.132, G.133, G.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100, A:D.100 EDO.6: 5 residues within 4Å: Chain A: T.140, I.142, P.144, F.164, R.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.210 EDO.7: 8 residues within 4Å: Chain A: I.5, G.7, S.8, T.9, I.10, A.59, K.60, E.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.9, A:E.63 EDO.8: 5 residues within 4Å: Chain A: F.39, D.42, L.43, T.195, T.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.39, A:T.196, A:T.196 EDO.9: 7 residues within 4Å: Chain A: L.32, G.33, I.55, D.56, A.57, A.86, A.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.33, A:D.56, A:A.57 Water bridges: A:N.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawai, A. et al., Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob.Agents Chemother. (2021)

Release Date

2021-08-11

Peptides

16S rRNA methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

16S rRNA methyltransferase