Structure of PDB 4dgt Chain B Binding Site BS01

Receptor Information

>4dgt Chain B (length=387) Species: 272563 (Clostridioides difficile 630)

NYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSL
KNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAIS
LLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMD
YEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDE
IHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPD
EKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNID
FAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVAL
NQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN

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: 4dgt Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dgt Crystal structures of putative aminotransferase from Clostridium difficile 630
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): G95 V96 I97 Y121 D200 I202 H203 K235
• Binding residue (residue number reindexed from 1): G94 V95 I96 Y120 D199 I201 H202 K234
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.4.1.13: cysteine-S-conjugate beta-lyase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016740 transferase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009058 biosynthetic process

External links

• PDB: RCSB:4dgt, PDBe:4dgt, PDBj:4dgt
• PDBsum: 4dgt
• UniProt: Q183G9