SMTL ID : 4me6.1

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.321, N.333, E.334 Ligands: ADP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.321, H2O.2, H2O.7 MG.3: 4 residues within 4Å: Chain B: D.321, N.333, E.334 Ligands: ADP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.321, H2O.9, H2O.13

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

ADP.2: 11 residues within 4Å: Chain A: F.202, K.204, E.240, A.241, A.242, V.243, E.247, F.323, N.333, E.334 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.204, A:E.240, A:A.241, A:V.243, A:E.247, A:N.333, A:E.334 Water bridges: A:E.247 Salt bridges: A:K.160, A:K.204 pi-Stacking: A:F.202, A:F.202 ADP.4: 11 residues within 4Å: Chain B: F.202, K.204, E.240, A.241, A.242, V.243, E.247, F.323, N.333, E.334 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.204, B:A.241, B:V.243, B:E.247, B:N.333 Salt bridges: B:K.160, B:K.204 pi-Stacking: B:F.202, B:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doan, T.N.N. et al., Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides. Arch.Biochem.Biophys. (2014)

Release Date

2014-02-19

Peptides

D-alanine--D-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-alanine--D-alanine ligase

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