SMTL ID : 3r5f.1

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: K.158, F.200, K.202, S.208, S.209, E.238, A.239, A.240, V.241, E.245, F.321, N.331, E.332 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.202, A:S.209, A:S.209, A:E.238, A:V.241, A:E.245, A:N.331, A:E.332 Water bridges: A:R.317 Salt bridges: A:K.158, A:K.202 pi-Stacking: A:F.200, A:F.200 ATP.3: 14 residues within 4Å: Chain B: K.158, F.200, K.202, S.208, S.209, E.238, A.239, A.240, V.241, E.245, F.321, N.331, E.332 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.202, B:S.209, B:S.209, B:E.238, B:E.238, B:V.241, B:E.245, B:N.331, B:E.332, B:E.332 Water bridges: B:E.245, B:R.317 Salt bridges: B:K.158, B:K.202 pi-Stacking: B:F.200, B:F.200

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.319, N.331, E.332 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.319, H2O.5 MG.4: 4 residues within 4Å: Chain B: D.319, N.331, E.332 Ligands: ATP.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.319, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doan, T.T.N. et al., Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP. To be Published

Release Date

2011-05-25

Peptides

D-alanine--D-alanine ligase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-alanine--D-alanine ligase 1

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