Structure of PDB 8ayk Chain B Binding Site BS01

Receptor Information

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

MNLCYIDGKFLPLEEAKLPVTDLIIQRGVGVFETISTHSRRPLMLTPHLK
RLEGSATASSIVMPATLDEMARIIREGIKKMGCETMVRPYITGGDSFGKD
HLFSSSRYFVIFEEIRKPDPILYEKGVALHPINAERYLPSTKSINYMLSF
TGQRDSKGAYEILYCPEGEIVEGSHSTFFLIKNGHLITAPTSRALSGTTR
QIVLELARRGNIQVEERCPLLTELPEAEEAFITGTVKELLPVVRIGDQII
GNGVPGKLTKHLHQVYLSSIVEWLE

Ligand information

• Ligand ID: PW0
• InChI: InChI=1S/C13H17N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4,18H,2-3,5-6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)
• InChIKey: AQYBBWUPMNWMHD-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Cc1ncc(CO[P](O)(O)=O)c(CN=C(CCC(O)=O)C(O)=O)c1O
  OpenEye OEToolkits 3.1.0.0: Cc1c(c(c(cn1)COP(=O)(O)O)CN=C(CCC(=O)O)C(=O)O)O
• Formula: C13 H17 N2 O9 P
• Name: (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid
• PDB chain: 8ayk Chain B Residue 301

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): T34 R51 R136 K142 Y146 E172 H175 S176 L195 T198 T199 G234 T235 V236 K237
• Binding residue (residue number reindexed from 1): T34 R51 R136 K142 Y146 E172 H175 S176 L195 T198 T199 G234 T235 V236 K237
• 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:8ayk, PDBe:8ayk, PDBj:8ayk
• PDBsum: 8ayk
• PubMed: 36903355
• UniProt: D5EHC5