Structure of PDB 3d2y Chain A Binding Site BS01

Receptor Information

>3d2y Chain A (length=257) Species: 511145 (Escherichia coli str. K-12 substr. MG1655)

EKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVS
SHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIE
LENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADI
APQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLL
ELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEAL
LEKYGQD

Ligand information

>3d2y Chain B (length=4)

gAEK

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d2y Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): Y36 T37 V53 W83 H84 A85 G86 N97 E104 H151 R158 K159 D161
• Binding residue (residue number reindexed from 1): Y32 T33 V49 W79 H80 A81 G82 N93 E100 H147 R154 K155 D157

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0008745 N-acetylmuramoyl-L-alanine amidase activity
• GO:0009392 N-acetyl-anhydromuramoyl-L-alanine amidase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009253 peptidoglycan catabolic process
• GO:0009254 peptidoglycan turnover
• GO:0071555 cell wall organization

Cellular Component

• GO:0009279 cell outer membrane
• GO:0019867 outer membrane

External links

• PDB: RCSB:3d2y, PDBe:3d2y, PDBj:3d2y
• PDBsum: 3d2y
• PubMed: 20036252
• UniProt: P75820|AMID_ECOLI N-acetylmuramoyl-L-alanine amidase AmiD (Gene Name=amiD)