SMTL ID : 8evz.1 (1 other biounit)

DdlB from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.225, R.265, D.267, E.280 Ligands: MG.2, ADP.3, DS0.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.267, A:E.280, H2O.2 MG.2: 6 residues within 4Å: Chain A: G.159, E.280, N.282 Ligands: MG.1, ADP.3, DS0.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.280, A:E.280, H2O.3 MG.5: 6 residues within 4Å: Chain B: G.159, E.280, N.282 Ligands: MG.6, ADP.7, DS0.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.280, B:E.280, H2O.6 MG.6: 7 residues within 4Å: Chain B: R.265, D.267, E.280, N.282 Ligands: MG.5, ADP.7, DS0.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.267, B:E.280, H2O.5

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

ADP.3: 24 residues within 4Å: Chain A: K.114, P.129, I.152, K.154, E.158, G.159, S.160, S.161, M.164, E.190, Q.191, W.192, I.193, E.197, F.219, Y.220, K.225, D.267, M.269, L.279, E.280 Ligands: MG.1, MG.2, DS0.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.154, A:S.160, A:S.161, A:E.190, A:I.193, A:E.197, A:Y.220, A:E.280, A:N.282 Water bridges: A:E.197, A:R.265, A:R.265, A:D.267 Salt bridges: A:K.114, A:K.114, A:K.154, A:K.225, A:K.225 ADP.7: 24 residues within 4Å: Chain B: K.114, P.129, I.152, K.154, E.158, G.159, S.160, S.161, M.164, E.190, Q.191, W.192, I.193, E.197, F.219, Y.220, K.225, D.267, M.269, L.279, E.280 Ligands: MG.5, MG.6, DS0.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.154, B:S.160, B:S.161, B:E.190, B:E.190, B:I.193, B:E.197, B:Y.220, B:D.267 Water bridges: B:E.197, B:K.225, B:K.225 Salt bridges: B:K.114, B:K.114, B:K.154, B:K.225

2 x DS0: [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate(Non-covalent)

DS0.4: 16 residues within 4Å: Chain A: E.32, H.80, E.85, G.159, S.160, K.225, Y.226, R.265, D.267, E.280, N.282, P.285, G.286 Ligands: MG.1, MG.2, ADP.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.160, A:R.265, A:N.282, A:N.282, A:G.286 Water bridges: A:H.80, A:H.80, A:K.114, A:R.265, A:R.265 Salt bridges: A:K.225, A:R.265 DS0.8: 15 residues within 4Å: Chain B: E.32, H.80, G.159, S.160, K.225, Y.226, R.265, D.267, E.280, N.282, P.285, G.286 Ligands: MG.5, MG.6, ADP.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.160, B:Y.226, B:R.265, B:N.282, B:G.286 Water bridges: B:K.225 Salt bridges: B:K.225, B:R.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pederick, J.L. et al., Comparative functional and structural analysis of Pseudomonas aeruginosa d-alanine-d-alanine ligase isoforms as prospective antibiotic targets. Febs J. (2023)

Release Date

2023-08-30

Peptides

D-alanine--D-alanine ligase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

D-alanine--D-alanine ligase B

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