Structure of PDB 8vkt Chain A Binding Site BS02

Receptor Information

>8vkt Chain A (length=383) Species: 1352 (Enterococcus faecium)

HMASMKKEEKIAILQEIIRIKSVNGNEGEVAAYLNKLLARHDITGEIVSY
RDGRDNLIARYQKGQSGKVLGLSGHMDVVAAGDESSWTYAPFAAEIHGNR
LYGRGATDMKSGLAAMVIAMIELKESGKPFNGTVKLLATVGEEVGELGGE
QLTKAGYVDDLDALIIGEPTNYSLMYTHMGSINYTVTSHGKEAHSSMPDQ
GYNAINHLNEFITKANAEMNHLAETIENPVLGKTIHNVTLISGGNQVNSI
PSHAQLQGNIRSIPEYPNDKIIALLQSIVNELNQETDYHLELMIDYNKIP
VKADPDSPLIHSIQQQFSQPLPLVGAAATTDAAEFTKANHSFDFVVFGPG
VVTLPHQVDEYVEIDNYLDMIEKYQGIILSYLA

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 8vkt Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vkt The three-dimensional structure of DapE from Enterococcus faecium reveals new insights into DapE/ArgE subfamily ligand specificity.
• Resolution: 1.398 Å
• Binding residue (original residue number in PDB): D104 E139 H352
• Binding residue (residue number reindexed from 1): D108 E143 H356
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.5.1.18: succinyl-diaminopimelate desuccinylase.

Gene Ontology

Molecular Function

• GO:0008777 acetylornithine deacetylase activity
• GO:0009014 succinyl-diaminopimelate desuccinylase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006526 L-arginine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate

External links

• PDB: RCSB:8vkt, PDBe:8vkt, PDBj:8vkt
• PDBsum: 8vkt
• PubMed: 38740150
• UniProt: A0A1S8KJG1