SMTL ID : 7u9k.1

Staphylococcus aureus D-alanine-D-alanine ligase in complex with ATP, D-ala-D-ala, Mg2+ and K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x DAL- DAL: DAL-DAL(Non-covalent)

DAL-DAL.1: 11 residues within 4Å: Chain B: E.16, V.19, H.96, S.183, K.251, Y.252, R.291, G.312, S.317, M.318 Ligands: ATP.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.19, B:K.251 Hydrogen bonds: B:E.16, B:S.183, B:Y.252, B:R.291, B:R.291, B:G.312, B:M.318 Salt bridges: B:R.291

4 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: S.127, E.306, T.307 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.127, A:T.307, H2O.5, H2O.6 K.5: 5 residues within 4Å: Chain B: R.291, D.293, N.305, E.306 Ligands: ATP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.293, B:E.306, H2O.8 K.6: 5 residues within 4Å: Chain B: S.127, E.306, T.307, N.308 Ligands: MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.127, B:T.307, H2O.7, H2O.10 K.7: 2 residues within 4Å: Chain B: N.171, Y.172 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.172

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.306 Ligands: ADP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.306, H2O.2, H2O.4, H2O.5 MG.8: 4 residues within 4Å: Chain B: E.306, N.308 Ligands: K.6, ATP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.306, B:E.306, H2O.8

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

ADP.4: 17 residues within 4Å: Chain A: K.130, L.145, F.175, K.177, G.182, S.183, S.184, I.187, E.213, Q.214, G.215, V.216, E.220, F.295, N.305, E.306 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.177, A:G.182, A:S.184, A:E.213, A:V.216, A:E.220, A:N.305, A:E.306 Water bridges: A:K.130, A:K.130 Salt bridges: A:K.130, A:K.130, A:K.177 pi-Stacking: A:F.175, A:F.175

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

ATP.9: 27 residues within 4Å: Chain B: K.130, L.145, F.175, K.177, G.182, S.183, S.184, I.187, E.213, Q.214, G.215, V.216, E.220, A.244, F.245, Y.246, K.251, R.291, D.293, F.295, N.305, E.306, N.308 Ligands: DAL-DAL.1, DAL-DAL.1, K.5, MG.8 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:K.177, B:L.181, B:S.183, B:S.184, B:E.213, B:E.213, B:V.216, B:E.220, B:Y.246, B:N.305, B:E.306, B:N.308 Water bridges: B:K.130, B:V.185, B:K.241, B:K.251, B:K.251 Salt bridges: B:K.130, B:K.130, B:K.177, B:K.251, B:K.251, B:K.251, B:R.291 pi-Stacking: B:F.175, B:F.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, R. et al., Structure-guided design and synthesis of ATP-competitive N-acyl-substituted sulfamide d-alanine-d-alanine ligase inhibitors. Bioorg.Med.Chem. (2023)

Release Date

2023-03-15

Peptides

D-alanine--D-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase

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