SMTL ID : 4l1k.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: K.158, A.173, F.200, K.202, S.208, S.209, V.212, E.238, A.239, A.240, V.241, E.245, F.321, N.331, E.332 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.202, A:S.208, A:E.238, A:V.241, A:E.245, A:N.331 Water bridges: A:E.245 Salt bridges: A:K.158, A:K.202 pi-Stacking: A:F.200, A:F.200 ANP.3: 16 residues within 4Å: Chain B: K.158, A.173, F.200, K.202, S.208, S.209, V.212, E.238, A.239, A.240, V.241, E.245, F.321, N.331, E.332 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.202, B:S.208, B:E.238, B:E.238, B:V.241, B:E.245, B:N.331 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: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.319, A:E.332 MG.4: 4 residues within 4Å: Chain B: D.319, N.331, E.332 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.319, B:E.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doan, T.T.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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