Structure of PDB 1c7n Chain D Binding Site BS01

Receptor Information

>1c7n Chain D (length=394) Species: 158 (Treponema denticola)

MIYDFTTKISRKNLGSLKWDLMYSQNPEVGNEVVPLSVADMEFKNPPELI
EGLKKYLDETVLGYTGPTEEYKKTVKKWMKDRHQWDIQTDWIINTAGVVP
AVFNAVREFTKPGDGVIIITPVYYPFFMAIKNQERKIIECELLEKDGYYT
IDFQKLEKLSKDKNNKALLFCSPHNPVGRVWKKDELQKIKDIVLKSDLML
WSDEIHFDLIMPGYEHTVFQSIDEQLADKTITFTAPSKTFNIAGMGMSNI
IIKNPDIRERFTKSRDATSGMPFTTLGYKACEICYKECGKWLDGCIKVID
KNQRIVKDFFEVNHPEIKAPLIEGTYLQWIDFRALKMDHKAMEEFMIHKA
QIFFDEGYIFGDGGIGFERINLAAPSSVIQESLERLNKALKDLK

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: 1c7n Chain D Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1c7n Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G97 V98 Y123 D203 I205 H206 S237 K238
• Binding residue (residue number reindexed from 1): G97 V98 Y123 D203 I205 H206 S237 K238
• Annotation score: 1

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0009058 biosynthetic process

External links

• PDB: RCSB:1c7n, PDBe:1c7n, PDBj:1c7n
• PDBsum: 1c7n
• PubMed: 10880431
• UniProt: Q56257