SMTL ID : 8evw.1

DdlA from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 26 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, R.285, D.287, R.289, L.299, E.300, N.302 Ligands: DAL.2, DAL.3, MG.4, MG.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.173, A:Q.177, A:S.179, A:T.180, A:E.209, A:V.212, A:E.216, A:F.240, A:Y.246, A:R.289 Water bridges: A:K.135, A:K.245, A:K.245 Salt bridges: A:K.135, A:K.135, A:K.173, A:K.245, A:K.245, A:K.245, A:R.285 ATP.6: 26 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, R.285, D.287, R.289, L.299, E.300, N.302 Ligands: DAL.7, DAL.8, MG.9, MG.10 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.173, B:Q.177, B:S.179, B:T.180, B:E.209, B:V.212, B:E.216, B:F.240, B:R.289, B:E.300 Water bridges: B:K.135, B:K.245, B:K.245 Salt bridges: B:K.135, B:K.135, B:K.173, B:K.245, B:K.245, B:K.245, B:R.285

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

DAL.2: 11 residues within 4Å: Chain A: E.19, V.22, H.101, S.179, Y.246, R.285, N.302, P.305, G.306 Ligands: ATP.1, DAL.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.22, A:H.101 Hydrogen bonds: A:E.19, A:R.285, A:R.285, A:G.306 DAL.3: 8 residues within 4Å: Chain A: K.245, Y.246, R.285, G.306, S.311, L.312 Ligands: ATP.1, DAL.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.245 Hydrogen bonds: A:Y.246, A:Y.246, A:G.306, A:L.312 Water bridges: A:R.285, A:L.313 Salt bridges: A:R.285 DAL.7: 10 residues within 4Å: Chain B: E.19, V.22, H.101, S.179, Y.246, R.285, P.305, G.306 Ligands: ATP.6, DAL.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.22, B:H.101 Hydrogen bonds: B:E.19, B:S.179, B:R.285, B:R.285, B:G.306 DAL.8: 8 residues within 4Å: Chain B: K.245, Y.246, R.285, G.306, S.311, L.312 Ligands: ATP.6, DAL.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.245 Hydrogen bonds: B:Y.246, B:Y.246, B:G.306, B:L.312 Water bridges: B:R.285, B:L.313 Salt bridges: B:R.285

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.300, N.302 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.300, A:E.300, H2O.4 MG.5: 4 residues within 4Å: Chain A: R.285, D.287, E.300 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.287, A:E.300, H2O.3 MG.9: 4 residues within 4Å: Chain B: E.300, N.302 Ligands: ATP.6, MG.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.300, B:E.300, H2O.23 MG.10: 5 residues within 4Å: Chain B: R.285, D.287, E.300 Ligands: ATP.6, MG.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.287, B:E.300, H2O.23

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

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