Structure of PDB 5ctv Chain A Binding Site BS03

Receptor Information

>5ctv Chain A (length=176) Species: 170187 (Streptococcus pneumoniae TIGR4)

ASMEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPE
LGFFSHIVGNGAIMQVGPVDNGAWDVGGGWNAETYAAVELIESHSTKEEF
MTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTAEYATNNQPNNHSDHV
DPYPYLAKWGISREQFKHDIENGLTI

Ligand information

• Ligand ID: AMV
• InChI: InChI=1S/C12H21NO8/c1-5(11(17)18)20-10-8(13-6(2)15)12(19-3)21-7(4-14)9(10)16/h5,7-10,12,14,16H,4H2,1-3H3,(H,13,15)(H,17,18)/t5-,7-,8-,9-,10-,12-/m1/s1
• InChIKey: UXEQYDNCHCKBIL-PKKPQKKZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C(=O)O)OC1C(C(OC(C1O)CO)OC)NC(=O)C
  OpenEye OEToolkits 1.5.0: C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1O)CO)OC)NC(=O)C
  CACTVS 3.341: CO[CH]1O[CH](CO)[CH](O)[CH](O[CH](C)C(O)=O)[CH]1NC(C)=O
  ACDLabs 10.04: O=C(O)C(OC1C(O)C(OC(OC)C1NC(=O)C)CO)C
  CACTVS 3.341: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H](C)C(O)=O)[C@H]1NC(C)=O
• Formula: C12 H21 N O8
• Name: methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside;
  METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE;
  methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucoside;
  methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-D-glucoside;
  methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-glucoside
• ZINC: ZINC000058650293
• PDB chain: 5ctv Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ctv 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.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): H26 S27 T28 E87 H147 D149
• Binding residue (residue number reindexed from 1): H28 S29 T30 E89 H149 D151
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.5.1.28: N-acetylmuramoyl-L-alanine amidase.

Gene Ontology

Molecular Function

• GO:0008745 N-acetylmuramoyl-L-alanine amidase activity

Biological Process

• GO:0009253 peptidoglycan catabolic process

External links

• PDB: RCSB:5ctv, PDBe:5ctv, PDBj:5ctv
• PDBsum: 5ctv
• PubMed: 27273793
• UniProt: P06653|ALYS_STRPN Autolysin (Gene Name=lytA)