Structure of PDB 3bm5 Chain A Binding Site BS01

Receptor Information

>3bm5 Chain A (length=338) Species: 294381 (Entamoeba histolytica HM-1:IMSS)

EQISISSPRKRIYHNILETIGGTPLVELHGVTEHPRIKKGTRILVKLEYF
NPMSSVKDRVGFNIVYQAIKDGRLKPGMEIIESTSGNTGIALCQAGAVFG
YRVNIAMPSTMSVERQMIMKAFGAELILTEGKKGMPGAIEEVNKMIKENP
GKYFVANQFGNPDNTAAHHYTANEIWEDTDGEVDIVVSAVGTSGTVIGVA
EKLKEKKKGIKIIAVEPEESAVLEGKAKGPHGIQGIGAGFIPDIYKKEFV
DEIIPIKTQDAWKMARAVVKYDGIMCGMSSGAAILAGLKEAEKPENEGKT
IVIIVPSCGERYLSTDLYKIKDEGTKIQILDSLLNEHH

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: 3bm5 Chain A Residue 342

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3bm5 Crystal structure of native O-acetyl-serine sulfhydrylase from Entamoeba histolytica and its complex with cysteine: structural evidence for cysteine binding and lack of interactions with serine acetyl transferase.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): K58 N88 G192 T193 S194 T196 G236 S280 P307
• Binding residue (residue number reindexed from 1): K57 N87 G191 T192 S193 T195 G235 S279 P306
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K58 S280
• Catalytic site (residue number reindexed from 1): K57 S279

Gene Ontology

Molecular Function

• GO:0004124 cysteine synthase activity

Biological Process

• GO:0006535 cysteine biosynthetic process from serine

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3bm5, PDBe:3bm5, PDBj:3bm5
• PDBsum: 3bm5
• PubMed: 18350570
• UniProt: O15570