Structure of PDB 8ayk Chain B Binding Site BS02

Receptor Information

>8ayk Chain B (length=275) Species: 81468 (Aminobacterium colombiense)

MNLCYIDGKFLPLEEAKLPVTDLIIQRGVGVFETISTHSRRPLMLTPHLK
RLEGSATASSIVMPATLDEMARIIREGIKKMGCETMVRPYITGGDSFGKD
HLFSSSRYFVIFEEIRKPDPILYEKGVALHPINAERYLPSTKSINYMLSF
TGQRDSKGAYEILYCPEGEIVEGSHSTFFLIKNGHLITAPTSRALSGTTR
QIVLELARRGNIQVEERCPLLTELPEAEEAFITGTVKELLPVVRIGDQII
GNGVPGKLTKHLHQVYLSSIVEWLE

Ligand information

• Ligand ID: PMP
• InChI: InChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)
• InChIKey: ZMJGSOSNSPKHNH-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1CN)C
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(CN)c1O
• Formula: C8 H13 N2 O5 P
• Name: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE;
  PYRIDOXAMINE-5'-PHOSPHATE
• ChEMBL: CHEMBL1235353
• DrugBank: DB02142
• ZINC: ZINC000001532708
• PDB chain: 8ayk Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ayk To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R51 K142 Y146 E172 S174 H175 S176 L195 T198 T199 T235
• Binding residue (residue number reindexed from 1): R51 K142 Y146 E172 S174 H175 S176 L195 T198 T199 T235
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008483 transaminase activity

Biological Process

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

External links

• PDB: RCSB:8ayk, PDBe:8ayk, PDBj:8ayk
• PDBsum: 8ayk
• PubMed: 36903355
• UniProt: D5EHC5