SMTL ID : 3n8d.1

Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 15 residues within 4Å: Chain A: L.145, F.175, K.177, S.183, S.184, I.187, E.213, Q.214, G.215, V.216, E.220, F.295, N.305, E.306 Ligands: SO4.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.177, A:S.183, A:S.184, A:E.213, A:E.213, A:V.216, A:E.220, A:N.305, A:E.306 Salt bridges: A:K.177 pi-Stacking: A:F.175, A:F.175 ANP.4: 12 residues within 4Å: Chain B: L.145, F.175, K.177, I.187, E.213, Q.214, G.215, V.216, E.220, F.295, N.305, E.306 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.177, B:E.213, B:V.216, B:E.220, B:D.293, B:N.305 Salt bridges: B:K.177 pi-Stacking: B:F.175, B:F.175

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.291, N.308, P.311, G.312 Ligands: ANP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.308, A:G.312 Water bridges: A:R.291, A:M.318 Salt bridges: A:R.291 SO4.5: 4 residues within 4Å: Chain B: R.291, N.308, P.311, G.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.308, B:G.312 Salt bridges: B:R.291

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

CL.3: 3 residues within 4Å: Chain A: N.228, D.229, Y.230 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meziane-Cherif, D. et al., Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9. J.Bacteriol. (2010)

Release Date

2010-10-13

Peptides

D-alanine--D-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase