SMTL ID : 5nri.2 (1 other biounit)

Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.226, Y.228, K.290 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.228, A:Y.228, A:K.290, A:K.290 Salt bridges: A:K.290 SO4.5: 6 residues within 4Å: Chain A: H.70, Y.221, R.260, N.277, P.280, G.281 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.221, A:Y.221, A:N.277, A:G.281 Water bridges: A:R.260, A:R.260, A:R.260, A:R.260, A:L.287 Salt bridges: A:H.70, A:R.260

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

EDO.2: 3 residues within 4Å: Chain A: A.240, R.244 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.244 EDO.3: 3 residues within 4Å: Chain A: A.236, A.237 Ligands: EDO.2 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: Q.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.113 EDO.8: 1 residues within 4Å: Chain A: R.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.207, A:R.207 EDO.9: 9 residues within 4Å: Chain A: V.25, S.26, S.29, A.68, L.69, H.70, A.279, P.280, G.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.25, A:S.29, A:A.279 Water bridges: A:M.282

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 16 residues within 4Å: Chain A: K.104, P.119, F.146, K.148, S.155, V.158, E.184, K.185, S.186, I.187, E.192, F.214, Y.215, M.264, L.274, E.275 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.148, A:E.184, A:I.187, A:E.192, A:Y.215, A:E.275, A:E.275 Water bridges: A:K.104, A:K.220, A:K.220, A:K.220, A:D.262 Salt bridges: A:K.104, A:K.148, A:K.220 pi-Stacking: A:F.146, A:F.146

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: R.293, G.298, Y.299, S.300, E.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.298, A:Y.299, A:S.300, A:E.301 Water bridges: A:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. Febs J. (2019)

Release Date

2018-05-30

Peptides

D-alanine--D-alanine ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D-alanine--D-alanine ligase

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