Structure of PDB 3kod Chain B Binding Site BS01

Receptor Information

>3kod Chain B (length=157) Species: 36329 (Plasmodium falciparum 3D7)

MRVVIQRVKGAILSVRKENEKELEIISEIKNGLICFLGIHKNDTWEDALY
IIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFH
LAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIY
IDTHDIN

Ligand information

• Ligand ID: DSN
• InChI: InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
• InChIKey: MTCFGRXMJLQNBG-UWTATZPHSA-N
• SMILES:
  CACTVS 3.341: N[CH](CO)C(O)=O
  OpenEye OEToolkits 1.5.0: C([C@H](C(=O)O)N)O
  CACTVS 3.341: N[C@H](CO)C(O)=O
  OpenEye OEToolkits 1.5.0: C(C(C(=O)O)N)O
  ACDLabs 10.04: O=C(O)C(N)CO
• Formula: C3 H7 N O3
• Name: D-SERINE
• ChEMBL: CHEMBL285123
• DrugBank: DB03929
• ZINC: ZINC000000895342
• PDB chain: 3kod Chain B Residue 165

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kod Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N66 T71 W72
• Binding residue (residue number reindexed from 1): N62 T67 W68
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): Q88 F89 T90
• Catalytic site (residue number reindexed from 1): Q84 F85 T86
• Enzyme Commision number: 3.1.1.96: D-aminoacyl-tRNA deacylase.

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0000166 nucleotide binding
• GO:0002161 aminoacyl-tRNA editing activity
• GO:0016787 hydrolase activity
• GO:0051499 D-aminoacyl-tRNA deacylase activity
• GO:0051500 D-tyrosyl-tRNA(Tyr) deacylase activity
• GO:0106026 Gly-tRNA(Ala) hydrolase activity

Biological Process

• GO:0006399 tRNA metabolic process
• GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3kod, PDBe:3kod, PDBj:3kod
• PDBsum: 3kod
• PubMed: 20007323
• UniProt: Q8IIS0|DTD_PLAF7 D-aminoacyl-tRNA deacylase (Gene Name=DTD)