SMTL ID : 3ham.2 (1 other biounit)

Structure of the gentamicin-APH(2")-IIa complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 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: 13 residues within 4Å: Chain A: D.192, S.194, N.196, D.213, C.225, D.228, S.230, D.232, D.262, W.265, Y.272, R.276 Ligands: GOL.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.232, A:Y.272 Hydrogen bonds: A:D.192, A:S.194, A:S.194, A:N.196, A:D.228, A:S.230, A:D.232, A:D.232, A:D.232, A:R.276 Water bridges: A:N.197, A:D.233, A:N.261, A:N.261 LLL.4: 11 residues within 4Å: Chain B: D.192, S.194, N.196, D.213, C.225, D.228, S.230, D.232, D.262, W.265, R.276 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:D.232 Hydrogen bonds: B:D.192, B:S.194, B:S.194, B:N.196, B:D.228, B:S.230, B:D.232, B:D.232, B:D.232, B:R.276, B:R.276 Water bridges: B:D.192, B:D.192, B:N.261, B:D.262

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.182, K.183, Y.184, P.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.184, A:Y.184 GOL.3: 5 residues within 4Å: Chain A: N.191, N.221, C.225, N.261 Ligands: LLL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.221, A:N.261 Water bridges: A:D.268, A:D.268 GOL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain B: Y.111, R.204, Y.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Young, P.G. et al., The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] provide insights into substrate selectivity in the APH(2'') subfamily. J.Bacteriol. (2009)

Release Date

2009-07-28

Peptides

Aminoglycoside phosphotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminoglycoside phosphotransferase

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