SMTL ID : 5ctv.1

Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

2 x ALA- DGL- LYS- DAL: fragment of peptidoglycan(Non-covalent)

ALA-DGL-LYS-DAL.1: 14 residues within 4Å: Chain A: E.50, L.51, G.52, F.54, W.74, D.75, V.76, G.77, N.81, E.89, H.146, S.147, H.149 Ligands: AMV-NAG-AMV-NAG.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.50, A:F.54, A:W.74, A:W.74, A:H.146 Hydrogen bonds: A:E.50, A:E.50, A:D.75, A:G.77, A:N.81, A:E.89 Water bridges: A:H.28, A:E.50, A:S.147, A:S.147, A:D.148 Salt bridges: A:H.149 ALA-DGL-LYS-DAL.2: 3 residues within 4Å: Chain A: H.34, N.39 Ligands: AMV-NAG-AMV-NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.34 Hydrogen bonds: A:N.39 Water bridges: A:N.32, A:N.39

1 x AMV- NAG- AMV- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside

AMV-NAG-AMV-NAG.3: 17 residues within 4Å: Chain A: H.28, S.29, T.30, N.32, N.39, E.40, Y.43, R.46, F.54, E.89, D.148, H.149, V.150, D.151 Ligands: ALA-DGL-LYS-DAL.1, ALA-DGL.2, ALA-DGL.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.54, A:D.151 Hydrogen bonds: A:H.28, A:T.30, A:D.148, A:V.150, A:D.151, A:D.151 Water bridges: A:K.47, A:D.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sandalova, T. et al., The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity. Mol.Microbiol. (2016)

Release Date

2016-06-15

Peptides

Autolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Autolysin