Structure of PDB 2wwd Chain A Binding Site BS03

Receptor Information

>2wwd Chain A (length=432) Species: 171101 (Streptococcus pneumoniae R6)

NAAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNY
YLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWG
YMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKV
GGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGEL
KEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKK
VIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENET
DAENDAKQTIELIKKYNMNLSYPIYYDVENWEYVNKSKRAPSDTDTWVKI
INKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEW
ENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY

Ligand information

• Ligand ID: CHT
• InChI: InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1
• InChIKey: OEYIOHPDSNJKLS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: C[N+](C)(C)CCO
  ACDLabs 10.04: OCC[N+](C)(C)C
• Formula: C5 H14 N O
• Name: CHOLINE ION
• ChEMBL: CHEMBL920
• DrugBank: DB00122
• ZINC: ZINC000003079337
• PDB chain: 2wwd Chain A Residue 609

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wwd Insights Into Pneumococcal Fratricide from the Crystal Structures of the Modular Killing Factor Lytc.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): W59 W68 Y86 M94
• Binding residue (residue number reindexed from 1): W23 W32 Y50 M58
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y117
• Catalytic site (residue number reindexed from 1): Y81
• Enzyme Commision number: 3.2.1.17: lysozyme.

Gene Ontology

Molecular Function

• GO:0003796 lysozyme activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0009253 peptidoglycan catabolic process
• GO:0016052 carbohydrate catabolic process
• GO:0016998 cell wall macromolecule catabolic process

External links

• PDB: RCSB:2wwd, PDBe:2wwd, PDBj:2wwd
• PDBsum: 2wwd
• PubMed: 20400948
• UniProt: Q8DP07