Structure of PDB 5yd2 Chain A Binding Site BS01

Receptor Information

>5yd2 Chain A (length=349) Species: 885315 (Entamoeba histolytica HM-3:IMSS)

IHNFGAMAKEVIEATAKAVNNFWEGLSILEISHRSKEWINVMNETKALMK
EVMDIPEGYEILFFGGGASLQFLMVAMNLLNKKACYLDTGVWASKAIKEA
ENIGEVKIIGTSKDKNYTYIPEYQIPSDYDYFHITTNNTIYGTEIRKDIE
SPIPLVADMSSDILSKPIDISKYSLIYAGAQKNCGAAGVTIVIIKKEILG
KVQRKIPIILDYQVHILNNSMYNTPPVISIFTVNQTLKYIKKIGGLKKIQ
ELNEEKARLLYAEIDRNKIFRGTVRKKDRSIMNVCFVMEEQYKQLENEFS
EYALQKGIIGIKGHRSVGGFRASIYNAVTIESVQALIKCMHDFEQLHTH

Ligand information

• Ligand ID: PLP
• InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
• InChIKey: NGVDGCNFYWLIFO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C=O)C
• Formula: C8 H10 N O6 P
• Name: PYRIDOXAL-5'-PHOSPHATE;
  VITAMIN B6 Phosphate
• ChEMBL: CHEMBL82202
• DrugBank: DB00114
• ZINC: ZINC000001532514
• PDB chain: 5yd2 Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yd2 N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): G72 A73 S74 W97 T144 D163 S165 K187
• Binding residue (residue number reindexed from 1): G67 A68 S69 W92 T139 D158 S160 K182
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.6.1.52: phosphoserine transaminase.

Gene Ontology

Molecular Function

• GO:0004648 O-phospho-L-serine:2-oxoglutarate aminotransferase activity
• GO:0008483 transaminase activity

Biological Process

• GO:0006563 L-serine metabolic process
• GO:0006564 L-serine biosynthetic process

External links

• PDB: RCSB:5yd2, PDBe:5yd2, PDBj:5yd2
• PDBsum: 5yd2
• PubMed: 30959130
• UniProt: M7XC02