Structure of PDB 2rd4 Chain A Binding Site BS01

Receptor Information

>2rd4 Chain A (length=119) Species: 195058 (Naja sagittifera)

NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNC
YNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICF
AGAPYNDNNYNIDLKARCQ

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 2rd4 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2rd4 Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution
• Resolution: 2.97 Å
• Binding residue (original residue number in PDB): D24 N112
• Binding residue (residue number reindexed from 1): D23 N111
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y28 G30 G32 H48 D49 Y52 Y68 D94
• Catalytic site (residue number reindexed from 1): Y27 G29 G31 H47 D48 Y51 Y67 D93
• Enzyme Commision number: 3.1.1.4: phospholipase A2.

Gene Ontology

Molecular Function

• GO:0004623 phospholipase A2 activity
• GO:0005509 calcium ion binding
• GO:0005543 phospholipid binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0047498 calcium-dependent phospholipase A2 activity

Biological Process

• GO:0006644 phospholipid metabolic process
• GO:0016042 lipid catabolic process
• GO:0050482 arachidonate secretion

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:2rd4, PDBe:2rd4, PDBj:2rd4
• PDBsum: 2rd4
• UniProt: P60043|PA2B1_NAJSG Basic phospholipase A2 1 (Fragment)