SMTL ID : 4c5c.1

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 27 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, Y.240, R.279, D.281, M.283, L.293, E.294, N.296 Ligands: DAL.2, DAL.3, MG.4, MG.5 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.168, A:G.173, A:S.174, A:S.175, A:E.204, A:L.207, A:E.211, A:Y.234, A:E.294, A:N.296 Water bridges: A:K.121, A:E.211, A:K.239, A:K.239, A:R.279 Salt bridges: A:K.121, A:K.121, A:K.168, A:K.239, A:K.239, A:K.239, A:R.279 ATP.9: 26 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, R.279, D.281, M.283, L.293, E.294, N.296 Ligands: DAL.10, DAL.11, MG.12, MG.13 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.168, B:G.173, B:S.174, B:S.175, B:E.204, B:L.207, B:E.211, B:Y.234, B:N.296 Water bridges: B:K.121, B:E.211, B:K.239, B:K.239, B:R.279 Salt bridges: B:K.121, B:K.121, B:K.168, B:K.239, B:K.239, B:K.239, B:R.279

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

DAL.2: 10 residues within 4Å: Chain A: E.39, V.42, H.87, S.174, Y.240, R.279, P.299, G.300 Ligands: ATP.1, DAL.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.42, A:H.87 Hydrogen bonds: A:E.39, A:R.279, A:R.279, A:G.300 DAL.3: 9 residues within 4Å: Chain A: Y.234, K.239, Y.240, R.279, G.300, S.305, L.306 Ligands: ATP.1, DAL.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.239, A:L.306 Hydrogen bonds: A:Y.240, A:Y.240, A:Y.240, A:G.300, A:L.306 Water bridges: A:V.307 Salt bridges: A:R.279 DAL.10: 10 residues within 4Å: Chain B: E.39, V.42, H.87, S.174, Y.240, R.279, P.299, G.300 Ligands: ATP.9, DAL.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.42, B:H.87 Hydrogen bonds: B:E.39, B:R.279, B:R.279, B:G.300 DAL.11: 9 residues within 4Å: Chain B: Y.234, K.239, Y.240, R.279, G.300, S.305, L.306 Ligands: ATP.9, DAL.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.239, B:L.306 Hydrogen bonds: B:Y.240, B:Y.240, B:Y.240, B:L.306 Water bridges: B:R.279, B:R.279 Salt bridges: B:R.279

7 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.121, E.294, N.296 Ligands: ATP.1, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.294, A:E.294, H2O.8 MG.5: 5 residues within 4Å: Chain A: K.239, D.281, E.294 Ligands: ATP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.281, A:E.294, H2O.11 MG.6: 1 residues within 4Å: Chain A: H.304 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.304, H2O.11, H2O.11, H2O.13, H2O.13, H2O.14 MG.12: 4 residues within 4Å: Chain B: E.294, N.296 Ligands: ATP.9, MG.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.294, B:E.294, H2O.20 MG.13: 5 residues within 4Å: Chain B: K.239, D.281, E.294 Ligands: ATP.9, MG.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.281, B:E.294, H2O.23 MG.14: 1 residues within 4Å: Chain B: H.304 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.304, H2O.23, H2O.23, H2O.23, H2O.25, H2O.25 MG.15: 1 residues within 4Å: Chain B: D.189 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: E.41, V.42, N.45, Y.236, Y.240, L.241, T.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.45, A:Y.236 GOL.8: 3 residues within 4Å: Chain A: Q.188, D.189, R.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.189, A:R.192 Water bridges: A:D.189

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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