Structure of PDB 8v05 Chain A Binding Site BS02

Receptor Information

>8v05 Chain A (length=426) Species: 10090 (Mus musculus)

GDLHLFGPNQRPAPCYDPCEAVLVESIPEGLEFPNATTSNPSTSQAWLGL
LAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLQQLQALAPRGVKVR
IAVSKPNGPLADLQSLLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYL
GSANMDWRSLTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPST
WPRSFDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNV
VDSARSFIYIAVMNYLPTMEFSHPRRFWPAIDDGLRRAAYERGVKVRLLI
SCWGHSDPSMRSFLLSLAALHDNHTHSDIQVKLFVVPTDESQARIPYARV
NHNKYMVTERASYIGTSNWSGSYFTETAGTSLLVTQNGHGGLRSQLEAVF
LRDWESPYSHDLDTSANSVGNACRLL

Ligand information

• Ligand ID: CYS
• InChI: InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
• InChIKey: XUJNEKJLAYXESH-REOHCLBHSA-N
• SMILES:
  CACTVS 3.341: N[CH](CS)C(O)=O
  OpenEye OEToolkits 1.5.0: C([C@@H](C(=O)O)N)S
  CACTVS 3.341: N[C@@H](CS)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CS
  OpenEye OEToolkits 1.5.0: C(C(C(=O)O)N)S
• Formula: C3 H7 N O2 S
• Name: CYSTEINE
• ChEMBL: CHEMBL863
• DrugBank: DB00151
• ZINC: ZINC000000895042
• PDB chain: 8v05 Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v05 Crystal structures of exonucleases PLD3 and PLD4
• Resolution: 2.08 Å
• Binding residue (original residue number in PDB): C280 G283 T284 P285
• Binding residue (residue number reindexed from 1): C218 G221 T222 P223
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.16.1: spleen exonuclease.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

External links

• PDB: RCSB:8v05, PDBe:8v05, PDBj:8v05
• PDBsum: 8v05
• PubMed: 38537643
• UniProt: O35405|PLD3_MOUSE 5'-3' exonuclease PLD3 (Gene Name=Pld3)