Structure of PDB 8onn Chain D Binding Site BS01

Receptor Information

>8onn Chain D (length=277) Species: 81468 (Aminobacterium colombiense)

GHMNLCYIDGKFLPLEEAKLPVTDLIIQRGVGVFETISTHSRRPLMLTPH
LKRLEGSATASSIVMPATLDEMARIIREGIKKMGCETMVRPYITGGDSFG
KDHLFSSSRYFVIFAEIRKPDPILYEKGVALHPINAERYLPSTKSINYML
SFTGQRDSKGAYEILYCPEGEIVEGSHSTFFLIKNGHLITAPTSRALSGT
TRQIVLELARRGNIQVEERCPLLTELPEAEEAFITGTVKELLPVVRIGDQ
IIGNGVPGKLTKHLHQVYLSSIVEWLE

Ligand information

• Ligand ID: OCF
• InChI: InChI=1S/C11H15N2O8P/c1-7-11(16)9(5-13-20-3-2-10(14)15)8(4-12-7)6-21-22(17,18)19/h4-5,16H,2-3,6H2,1H3,(H,14,15)(H2,17,18,19)/b13-5+
• InChIKey: WFKOVQOIGDESOJ-WLRTZDKTSA-N
• SMILES:
  CACTVS 3.385: Cc1ncc(CO[P](O)(O)=O)c(\C=N\OCCC(O)=O)c1O
  OpenEye OEToolkits 3.1.0.0: Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/OCCC(=O)O)O
  OpenEye OEToolkits 3.1.0.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=NOCCC(=O)O)O
  CACTVS 3.385: Cc1ncc(CO[P](O)(O)=O)c(C=NOCCC(O)=O)c1O
• Formula: C11 H15 N2 O8 P
• Name: 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid;
  PYRIDOXAMINE-5'-PHOSPHATE linked to 3-aminooxypropionic acid
• PDB chain: 8onn Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8onn In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): T34 K142 Y146 S174 H175 S176 L195 T198 T199 G234 T235 V236 K237
• Binding residue (residue number reindexed from 1): T36 K144 Y148 S176 H177 S178 L197 T200 T201 G236 T237 V238 K239
• Annotation score: 1

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:8onn, PDBe:8onn, PDBj:8onn
• PDBsum: 8onn
• PubMed: 37548495
• UniProt: D5EHC5