SMTL ID : 5nri.1 (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

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: K.104, P.119, F.146, K.148, 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:E.184, A:I.187, A:E.192, A:Y.215, A:E.275, A:E.275 Water bridges: A:K.104, A:E.192, A:K.220, A:K.220 Salt bridges: A:K.104, A:K.148, A:K.220 pi-Stacking: A:F.146, A:F.146

2 x DAL: D-ALANINE(Non-covalent)

DAL.2: 7 residues within 4Å: Chain A: R.260, P.280, G.281, S.286, L.287, P.288 Ligands: DAL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.260, A:G.281, A:L.287 Water bridges: A:S.286 Salt bridges: A:R.260 DAL.3: 8 residues within 4Å: Chain A: H.70, R.260, N.277, A.279, P.280, G.281 Ligands: DAL.2, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.277, A:G.281 Water bridges: A:H.70, A:H.70, A:K.220, A:R.260, A:N.277

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: H.70, E.75 Ligands: DAL.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.70, H2O.1, H2O.6, H2O.9, H2O.14

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

SO4.5: 3 residues within 4Å: Chain A: R.293, G.298, Y.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.299 Water bridges: A:R.293, A:R.293, A:S.300 Salt bridges: A:R.293

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

EDO.6: 3 residues within 4Å: Chain A: L.109, Q.112, F.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.112 Water bridges: A:T.123, A:T.123 EDO.7: 2 residues within 4Å: Chain A: K.11, H.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.11 EDO.8: 2 residues within 4Å: Chain A: R.126, K.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126, A:K.179

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
A

D-alanine--D-alanine ligase

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