SMTL ID : 2c1g.1

Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 10 residues within 4Å: Chain A: D.243, D.244, H.294, H.298, P.334, Y.335, W.353, H.385 Ligands: ZN.2, PEG.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.353 Hydrogen bonds: A:D.243, A:Y.335 Salt bridges: A:H.294, A:H.298, A:H.385

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.243, D.244, H.294, H.298 Ligands: ACT.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.244, A:H.294, A:H.298, ACT.1, H2O.7 ZN.3: 3 residues within 4Å: Chain A: Q.101, E.112, E.114 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.112, A:E.112, A:E.114, H2O.7 ZN.4: 2 residues within 4Å: Chain A: D.347, H.423 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.423

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: Y.335, W.353, W.360 Ligands: ACT.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blair, D.E. et al., Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Proc. Natl. Acad. Sci. U.S.A. (2005)

Release Date

2005-09-15

Peptides

PEPTIDOGLYCAN GLCNAC DEACETYLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PEPTIDOGLYCAN GLCNAC DEACETYLASE