SMTL ID : 5jip.1

Crystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 13 residues within 4Å: Chain A: D.18, N.20, R.41, Y.73, F.75, D.113, E.115, Y.149, W.176, Y.180, Q.203, D.218 Ligands: MES.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.20, A:Q.203 Salt bridges: A:R.41, A:D.113, A:E.115 MES.2: 12 residues within 4Å: Chain A: E.115, Y.149, G.151, L.152, F.153, A.178, M.179, Y.180, I.183, N.186, Q.203 Ligands: MES.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.152, A:F.153, A:Y.180, A:N.186 Water bridges: A:E.115 MES.4: 12 residues within 4Å: Chain B: D.18, N.20, R.41, Y.73, F.75, D.113, E.115, Y.149, Y.180, Q.203, D.218 Ligands: MES.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.20, B:Y.73, B:Y.73, B:Q.203 Water bridges: B:E.115 Salt bridges: B:R.41, B:D.113, B:E.115 MES.5: 12 residues within 4Å: Chain B: E.115, Y.149, G.151, L.152, F.153, A.178, M.179, Y.180, I.183, N.186, Q.203 Ligands: MES.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.152, B:F.153, B:Y.180, B:N.186 Water bridges: B:G.151

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.227, S.228, M.230, P.231, D.258, D.304 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.227, A:M.230, A:D.258, A:D.304, H2O.2, H2O.4 MG.6: 7 residues within 4Å: Chain B: D.227, S.228, M.230, P.231, P.232, D.258, D.304 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.227, B:M.230, B:D.258, B:D.304, H2O.25, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Al-Riyami, B. et al., The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination. Proteins (2016)

Release Date

2016-08-10

Peptides

Cortical-lytic enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cortical-lytic enzyme