Structure of PDB 3b1d Chain C Binding Site BS01

Receptor Information

>3b1d Chain C (length=386) Species: 1328 (Streptococcus anginosus)

KYNFQTAPNRLSHHTYKWKETETDPQLLPAWIADMDFEVMPEVKQAIHDY
AEQLVYGYTYASDELLQAVLDWEKSEHQYSFDKEDIVFVEGVVPAISIAI
QAFTKEGEAVLINSPVYPPFARSVRLNNRKLVSNSLKEENGLFQIDFEQL
ENDIVENDVKLYLLCNPHNPGGRVWEREVLEQIGHLCQKHHVILVSDEIH
QDLTLFGHEHVSFNTVSPDFKDFALVLSSATKTFNIAGTKNSYAIIENPT
LCAQFKHQQLVNNHHEVSSLGYIATETAYRYGKPWLVALKAVLEENIQFA
VEYFAQEAPRLKVMKPQGTYLIWLDFSDYGLTDDALFTLLHDQAKVILNR
GSDYGSEGELHARLNIAAPKSLVEEICKRIVCCLPK

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: 3b1d Chain C Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3b1d Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
• Resolution: 1.66 Å
• Binding residue (original residue number in PDB): G93 V94 V95 Y119 D199 I201 H202 K234
• Binding residue (residue number reindexed from 1): G91 V92 V93 Y117 D197 I199 H200 K232
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y119 D199 I201
• Catalytic site (residue number reindexed from 1): Y117 D197 I199
• Enzyme Commision number: 4.4.1.13: cysteine-S-conjugate beta-lyase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0009058 biosynthetic process

External links

• PDB: RCSB:3b1d, PDBe:3b1d, PDBj:3b1d
• PDBsum: 3b1d
• PubMed: 22674431
• UniProt: A6BMJ3