Structure of PDB 8raf Chain A Binding Site BS01

Receptor Information

>8raf Chain A (length=281) Species: 760192 (Haliscomenobacter hydrossis DSM 1100)

MIKYYNINGQQVPVENATLHVSDLSILRGYGIFDYFLAREGHPLFLDDYL
NRFYRSAAELYLEIPFDKAELRRQIYALLQANEVREAGIILVLTGGYSPD
GYTPVNPNLLIMMYDLPASAWEFSAQGIKIITHPFQRELPEVKTINYSTG
IRMLKTIKERGATDLIYVDQGEWIRESARSNFFLVMPDNTIVTADEKILW
GITRRQVIDAAREAGYAVEERRIHITELDQAREAFFTSTIKGVMAIGQID
DRVFGDGTIGKVTQELQDLFVGKVKAYLETC

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: 8raf Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8raf nraveling the role of active site arginines in a non-canonical D-amino acid transaminase from Haliscomenobacter hydrossis
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R52 R137 K143 Y147 E176 A178 R179 S180 G201 I202 T203 T239
• Binding residue (residue number reindexed from 1): R52 R137 K143 Y147 E176 A178 R179 S180 G201 I202 T203 T239
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008483 transaminase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0019752 carboxylic acid metabolic process
• GO:0046394 carboxylic acid biosynthetic process

External links

• PDB: RCSB:8raf, PDBe:8raf, PDBj:8raf
• PDBsum: 8raf
• PubMed: 38649133
• UniProt: F4KWH0