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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

DAL.1: 10 residues within 4Å: Chain A: E.32, V.35, H.80, S.160, Y.226, R.265, N.282, G.286 Ligands: DAL.2, ATP.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.35 Hydrogen bonds: A:E.32, A:S.160, A:R.265, A:R.265, A:G.286 DAL.2: 8 residues within 4Å: Chain A: K.225, Y.226, R.265, G.286, S.291, L.292 Ligands: DAL.1, ATP.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.225, A:L.292 Hydrogen bonds: A:Y.226, A:Y.226, A:Y.226, A:G.286, A:L.292 Water bridges: A:R.265 Salt bridges: A:R.265 DAL.6: 10 residues within 4Å: Chain B: E.32, V.35, H.80, S.160, Y.226, R.265, N.282, G.286 Ligands: DAL.7, ATP.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.35 Hydrogen bonds: B:E.32, B:S.160, B:R.265, B:R.265, B:G.286 Water bridges: B:H.80 DAL.7: 8 residues within 4Å: Chain B: K.225, Y.226, R.265, G.286, S.291, L.292 Ligands: DAL.6, ATP.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.225, B:L.292 Hydrogen bonds: B:Y.226, B:Y.226, B:G.286, B:L.292 Water bridges: B:R.265 Salt bridges: B:R.265

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: R.265, D.267, E.280, N.282 Ligands: MG.4, ATP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.267, A:E.280, H2O.2 MG.4: 5 residues within 4Å: Chain A: K.114, E.280, N.282 Ligands: MG.3, ATP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.280, A:E.280, H2O.3 MG.8: 6 residues within 4Å: Chain B: R.265, D.267, E.280, N.282 Ligands: MG.9, ATP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.267, B:E.280, H2O.6 MG.9: 5 residues within 4Å: Chain B: K.114, E.280, N.282 Ligands: MG.8, ATP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.280, B:E.280, H2O.7

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

ATP.5: 26 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, R.265, D.267, L.279, E.280, N.282 Ligands: DAL.1, DAL.2, MG.3, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:K.154, A:G.159, A:S.160, A:S.161, A:E.190, A:E.190, A:I.193, A:E.197, A:Y.220, A:E.280, A:E.280, A:N.282 Water bridges: A:K.114, A:I.162, A:I.162, A:E.197, A:R.265, A:R.265 Salt bridges: A:K.114, A:K.114, A:K.154, A:K.225, A:K.225, A:K.225, A:R.265 ATP.10: 26 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, R.265, D.267, L.279, E.280, N.282 Ligands: DAL.6, DAL.7, MG.8, MG.9 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:K.154, B:G.159, B:S.160, B:S.161, B:E.190, B:I.193, B:E.197, B:Y.220, B:E.280, B:N.282 Water bridges: B:K.114, B:I.162, B:I.162, B:E.197, B:E.197, B:R.265, B:R.265 Salt bridges: B:K.114, B:K.114, B:K.154, B:K.225, B:K.225, 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
B

B
B

D-alanine--D-alanine ligase B

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