SMTL ID : 4c5a.1

The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

1 x GLU- ASN- LEU- TYR- PHE- GLN- GLY- ALA: PEPTIDE(Non-covalent)

GLU-ASN-LEU-TYR-PHE-GLN-GLY-ALA.1: 9 residues within 4Å: Chain A: M.25, T.26, K.28, R.55, G.58, I.59, D.60, Y.62, M.77 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.26, A:R.55, A:R.55 Hydrogen bonds: A:M.25, A:D.60, A:Y.62, A:Y.62 Water bridges: A:K.28 Salt bridges: A:K.28

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

ADP.2: 23 residues within 4Å: Chain A: K.121, I.166, K.168, E.172, G.173, S.174, S.175, M.178, E.204, K.205, W.206, L.207, E.211, F.233, Y.234, K.239, D.281, M.283, L.293, E.294 Ligands: DS0.3, MG.4, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.168, A:G.173, A:S.174, A:S.175, A:E.204, A:E.204, A:L.207, A:E.211, A:Y.234 Water bridges: A:E.211, A:E.211, A:D.281 Salt bridges: A:K.121, A:K.121, A:K.168, A:K.239, A:K.239 ADP.8: 22 residues within 4Å: Chain B: K.121, I.166, K.168, E.172, G.173, S.174, S.175, M.178, E.204, K.205, W.206, L.207, E.211, F.233, Y.234, K.239, D.281, M.283, E.294 Ligands: DS0.9, MG.10, MG.11 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.168, B:G.173, B:S.174, B:S.175, B:E.204, B:E.204, B:L.207, B:E.211, B:Y.234, B:E.294 Water bridges: B:K.239, B:K.239 Salt bridges: B:K.121, B:K.121, B:K.168, B:K.239, B:K.239

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

DS0.3: 15 residues within 4Å: Chain A: E.39, H.87, G.173, S.174, K.239, Y.240, R.279, D.281, E.294, N.296, P.299, G.300 Ligands: ADP.2, MG.4, MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.174, A:R.279, A:N.296, A:G.300 Water bridges: A:E.92, A:K.121, A:R.279, A:N.296, A:N.296 Salt bridges: A:K.239, A:R.279 DS0.9: 15 residues within 4Å: Chain B: E.39, H.87, G.173, S.174, K.239, Y.240, R.279, D.281, E.294, N.296, P.299, G.300 Ligands: ADP.8, MG.10, MG.11 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.174, B:Y.240, B:R.279, B:N.296, B:N.296, B:G.300 Water bridges: B:K.239, B:K.239, B:K.239, B:K.239, B:R.279 Salt bridges: B:K.239, B:R.279 pi-Stacking: B:H.87

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: K.121, G.173, E.294, N.296 Ligands: ADP.2, DS0.3, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.294, A:E.294, H2O.6 MG.5: 7 residues within 4Å: Chain A: K.239, D.281, E.294, N.296 Ligands: ADP.2, DS0.3, MG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.281, A:E.294 MG.10: 6 residues within 4Å: Chain B: G.173, E.294, N.296 Ligands: ADP.8, DS0.9, MG.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.294, B:E.294 MG.11: 6 residues within 4Å: Chain B: K.239, D.281, E.294 Ligands: ADP.8, DS0.9, MG.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.281, B:E.294, H2O.13

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.41, V.42, N.45, Y.236, L.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.45, A:Y.236 Water bridges: A:E.41 GOL.7: 4 residues within 4Å: Chain A: N.185, Q.188, D.189, R.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.189, A:R.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batson, S. et al., Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun (2017)

Release Date

2015-01-21

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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