SMTL ID : 8evx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: K.135, V.171, K.173, Q.177, G.178, S.179, T.180, L.183, E.209, R.210, F.211, V.212, E.216, V.239, F.240, K.245, D.287, R.289, L.299, E.300 Ligands: DS0.2, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.173, A:G.178, A:S.179, A:T.180, A:E.209, A:V.212, A:E.216, A:F.240, A:D.287, A:R.289 Water bridges: A:Q.177, A:K.245, A:K.245, A:N.302 Salt bridges: A:K.135, A:K.135, A:K.173, A:K.245, A:K.245 ADP.6: 23 residues within 4Å: Chain B: K.135, V.171, K.173, Q.177, G.178, S.179, T.180, L.183, E.209, R.210, F.211, V.212, E.216, V.239, F.240, K.245, D.287, R.289, L.299, E.300 Ligands: DS0.7, MG.8, MG.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.173, B:G.178, B:S.179, B:T.180, B:E.209, B:V.212, B:E.216, B:F.240, B:D.287, B:R.289 Water bridges: B:K.245, B:K.245 Salt bridges: B:K.135, B:K.135, B:K.173, B:K.245, B:K.245

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

DS0.2: 16 residues within 4Å: Chain A: E.19, H.101, G.178, S.179, K.245, Y.246, R.285, D.287, E.300, N.302, L.304, P.305, G.306 Ligands: ADP.1, MG.3, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.179, A:Y.246, A:R.285, A:N.302, A:N.302, A:G.306 Water bridges: A:K.135, A:K.245, A:R.285, A:D.287 Salt bridges: A:K.245, A:R.285 DS0.7: 16 residues within 4Å: Chain B: E.19, H.101, G.178, S.179, K.245, Y.246, R.285, D.287, E.300, N.302, L.304, P.305, G.306 Ligands: ADP.6, MG.8, MG.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.179, B:Y.246, B:R.285, B:N.302, B:N.302, B:G.306 Water bridges: B:K.245, B:R.285 Salt bridges: B:K.245, B:R.285

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: K.135, E.300, N.302 Ligands: ADP.1, DS0.2, MG.4, K.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.300, A:E.300, H2O.5 MG.4: 7 residues within 4Å: Chain A: K.245, D.287, E.300, N.302 Ligands: ADP.1, DS0.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.287, A:E.300, H2O.5 MG.8: 6 residues within 4Å: Chain B: E.300, N.302 Ligands: ADP.6, DS0.7, MG.9, K.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.300, B:E.300, H2O.17 MG.9: 7 residues within 4Å: Chain B: K.245, D.287, E.300, N.302 Ligands: ADP.6, DS0.7, MG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.287, B:E.300, H2O.17

2 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: A.132, E.300, V.301, N.302 Ligands: MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.132, A:E.300, A:V.301, H2O.4, H2O.5 K.10: 6 residues within 4Å: Chain B: A.132, M.133, E.300, V.301, N.302 Ligands: MG.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.132, B:E.300, B:V.301, H2O.15, H2O.16

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 A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase A