Structure of PDB 5ypd Chain A Binding Site BS01

Receptor Information

>5ypd Chain A (length=282) Species: 419947 (Mycobacterium tuberculosis H37Ra)

RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVA
GRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKS
CNTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVA
DEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFT
GHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDD
GWTVVTKDRKWTAQFEHTLLVTDTGVEILTAL

Ligand information

• Ligand ID: CO
• InChI: InChI=1S/Co/q+2
• InChIKey: XLJKHNWPARRRJB-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Co+2]
  CACTVS 3.341: [Co++]
• Formula: Co
• Name: COBALT (II) ION
• DrugBank: DB14205
• PDB chain: 5ypd Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ypd Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity.
• Resolution: 1.62 Å
• Binding residue (original residue number in PDB): D142 H205 T236 E238 E269
• Binding residue (residue number reindexed from 1): D139 H202 T233 E235 E266
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 3.4.11.18: methionyl aminopeptidase.

Gene Ontology

Molecular Function

• GO:0004177 aminopeptidase activity
• GO:0004239 initiator methionyl aminopeptidase activity
• GO:0008235 metalloexopeptidase activity
• GO:0046872 metal ion binding
• GO:0046914 transition metal ion binding
• GO:0070006 metalloaminopeptidase activity

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5ypd, PDBe:5ypd, PDBj:5ypd
• PDBsum: 5ypd
• PubMed: 30763644
• UniProt: A5U6L5