Structure of PDB 5eqv Chain A Binding Site BS01

Receptor Information

>5eqv Chain A (length=336) Species: 214092 (Yersinia pestis CO92)

AATVDLRVLETTDLHSNMMDFDYYKDKPTEKFGLVRTASLIIAARQQATN
SVLVDNGDVIQGSPLGDYIAAKGLNDGEIHPVYKAMNTLDYAVGNIGNHE
FNYGLDYLKKSLAGAKFPYVNANVIDVKTGKPLFQPYLIIDTPVKDRDGK
SHNLRIGYIGFVPPQVMIWDKANLSGKVTVNDITETAKKWVPEMREQGAD
LVVAIPHSGLSSDPYKTMAENSVYYLSQVPGIDAIMFGHAHGVFPSKDFA
AIKGADITQGTLNGIPAVMPGQWGDHLGVVDFVLNNDQGKWQVIDAKAEA
RPIYDKTAQKSLAAENAKLVEVLAVDHQSTRDFVSQ

Ligand information

• Ligand ID: FE
• InChI: InChI=1S/Fe/q+3
• InChIKey: VTLYFUHAOXGGBS-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: [Fe+3]
• Formula: Fe
• Name: FE (III) ION
• DrugBank: DB13949
• PDB chain: 5eqv Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5eqv 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site.
• Resolution: 1.45 Å
• Binding residue (original residue number in PDB): D84 N124 H233 H265
• Binding residue (residue number reindexed from 1): D58 N98 H207 H239
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D39 H41 D84 N124 H125 N128 H233 H265 H267
• Catalytic site (residue number reindexed from 1): D13 H15 D58 N98 H99 N102 H207 H239 H241
• Enzyme Commision number: 3.1.3.6: 3'-nucleotidase.
  3.1.4.16: 2',3'-cyclic-nucleotide 2'-phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016787 hydrolase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0009166 nucleotide catabolic process

External links

• PDB: RCSB:5eqv, PDBe:5eqv, PDBj:5eqv
• PDBsum: 5eqv
• UniProt: A0A5P8YBY3