SMTL ID : 3mfd.1 (1 other biounit)

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 8 residues within 4Å: Chain A: S.36, S.68, S.91, K.181, K.196, T.197, G.198, Y.199 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.199 Hydrogen bonds: A:S.36, A:S.36, A:S.68, A:S.68, A:S.68, A:R.90, A:S.91, A:K.181, A:T.197, A:Y.199 Water bridges: A:S.68, A:K.196, A:T.197 Salt bridges: A:K.39, A:K.181, A:K.181, A:K.196, A:K.196 CIT.5: 2 residues within 4Å: Chain A: R.90, K.179 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.90, A:R.90 Water bridges: A:K.179, A:K.183, A:K.183, A:K.183 Salt bridges: A:R.90, A:R.90, A:K.179, A:K.183 CIT.7: 4 residues within 4Å: Chain A: K.167, I.168, K.179, T.186 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.167, A:K.179, A:K.179 Salt bridges: A:K.167, A:K.179

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: H.140, Y.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.31, A:N.139, A:H.140 Water bridges: A:H.140 EDO.3: 6 residues within 4Å: Chain A: M.52, K.81, Y.85, D.159, K.162, I.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.85 Water bridges: A:K.81, A:K.81 EDO.4: 3 residues within 4Å: Chain A: H.29, K.124, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.124, A:N.125 Water bridges: A:K.124 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuff, M.E. et al., The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis. TO BE PUBLISHED

Release Date

2010-05-19

Peptides

D-alanyl-D-alanine carboxypeptidase dacB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-alanyl-D-alanine carboxypeptidase dacB

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