Structure of PDB 5vo3 Chain A Binding Site BS04

Receptor Information

>5vo3 Chain A (length=380) Species: 727 (Haemophilus influenzae)

ASNAMKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFN
DTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGR
GAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVV
ETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQGHVA
YPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNV
IPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLT
KPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNS
TIHKVNECVSVEDLGKCGEIYHKMLVNLLD

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: 5vo3 Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vo3 Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.
• Resolution: 1.954 Å
• Binding residue (original residue number in PDB): D100 E135 H349
• Binding residue (residue number reindexed from 1): D104 E139 H353
• Annotation score: 1

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0009014 succinyl-diaminopimelate desuccinylase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0050897 cobalt ion binding

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate
• GO:0019877 diaminopimelate biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5vo3, PDBe:5vo3, PDBj:5vo3
• PDBsum: 5vo3
• PubMed: 29272107
• UniProt: P44514|DAPE_HAEIN Succinyl-diaminopimelate desuccinylase (Gene Name=dapE)