SMTL ID : 4fu0.1

Crystal Structure of VanG D-Ala:D-Ser Ligase from Enterococcus faecalis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: K.140, F.181, K.183, S.190, I.193, E.219, E.220, T.221, I.222, E.226, L.247, Y.258, K.261, F.301, N.311, E.312 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.183, A:S.190, A:E.219, A:I.222, A:E.226, A:N.311, A:E.312 Water bridges: A:E.226, A:E.226, A:K.261, A:R.297, A:R.297, A:D.299, A:D.299, A:E.312 Salt bridges: A:K.140, A:K.140, A:K.183, A:K.261, A:K.261 pi-Stacking: A:F.181, A:F.181 ADP.6: 15 residues within 4Å: Chain B: K.140, F.181, K.183, S.190, I.193, E.219, E.220, T.221, I.222, E.226, L.247, F.252, F.301, N.311, E.312 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.183, B:E.219, B:E.219, B:I.222, B:E.226, B:N.311, B:E.312, B:E.312 Water bridges: B:K.140, B:E.226 Salt bridges: B:K.140, B:K.183 pi-Stacking: B:F.181, B:F.181

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

SO4.2: 5 residues within 4Å: Chain A: R.297, N.314, P.317, G.318, R.324 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.314, A:G.318 Water bridges: A:R.297, A:R.324, A:R.324, A:R.324, A:R.324, A:Y.325 Salt bridges: A:R.297, A:R.324 SO4.3: 4 residues within 4Å: Chain A: N.223, T.303, P.304, S.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.305, A:S.305 Water bridges: A:N.223 SO4.4: 2 residues within 4Å: Chain A: S.335, F.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.336 Water bridges: A:S.337 Salt bridges: A:K.330 SO4.5: 3 residues within 4Å: Chain A: K.108, G.188, S.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.188, A:S.189 Salt bridges: A:K.108 SO4.7: 4 residues within 4Å: Chain B: R.297, G.318, S.323, R.324 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.318, B:R.324 Water bridges: B:G.318, B:S.323, B:R.324, B:Y.325 Salt bridges: B:R.297 SO4.8: 4 residues within 4Å: Chain B: N.223, T.303, P.304, S.305 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.303, B:T.303, B:S.305, B:S.305 Water bridges: B:N.223 SO4.9: 4 residues within 4Å: Chain B: A.187, G.188, S.189, H.212 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.188, B:S.189, B:S.189 Salt bridges: B:H.212 SO4.10: 3 residues within 4Å: Chain B: K.264, Y.266, R.270 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.264, B:R.270 SO4.11: 3 residues within 4Å: Chain B: K.330, S.335, F.336 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.336 Water bridges: B:L.334, B:S.335 Salt bridges: B:K.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meziane-Cherif, D. et al., Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis. J.Biol.Chem. (2012)

Release Date

2012-09-19

Peptides

D-alanine--D-alanine ligase 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase 7