Structure of PDB 3p8y Chain B Binding Site BS01

Receptor Information

>3p8y Chain B (length=294) Species: 29292 (Pyrococcus abyssi)

MNAVEIISRDIYKAIDIQTKILDYMTKFFTDRGFKWLLPIMLSPITDPLW
PDPAGEGIRPAEVDVYGVRMRLTHSMILHKQLAIAMGLEKIFVLSPNIRL
ESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEELIYGLFRKAEEWTGR
EFPRARHFKVYDYKDILEEFGSDEKASMEMEEPFWIVNIPREFYDREENG
VWKNYDLILPYGYGEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIA
RAGKLKPSAGAGIGVERLVRFIVGAKHIAEVQPFPRVPGIPAVI

Ligand information

• Ligand ID: ASN
• InChI: InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1
• InChIKey: DCXYFEDJOCDNAF-REOHCLBHSA-N
• SMILES:
  CACTVS 3.370: N[C@@H](CC(N)=O)C(O)=O
  ACDLabs 12.01: O=C(N)CC(N)C(=O)O
  CACTVS 3.370: N[CH](CC(N)=O)C(O)=O
  OpenEye OEToolkits 1.7.2: C(C(C(=O)O)N)C(=O)N
  OpenEye OEToolkits 1.7.2: C([C@@H](C(=O)O)N)C(=O)N
• Formula: C4 H8 N2 O3
• Name: ASPARAGINE
• ChEMBL: CHEMBL58832
• DrugBank: DB00174
• ZINC: ZINC000001532556
• PDB chain: 3p8y Chain B Residue 295

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3p8y Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Q116 Y194 S218 G219 R222 A261 G262
• Binding residue (residue number reindexed from 1): Q116 Y194 S218 G219 R222 A261 G262
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R99 E101 R109 H110
• Catalytic site (residue number reindexed from 1): R99 E101 R109 H110

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004816 asparagine-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006421 asparaginyl-tRNA aminoacylation

External links

• PDB: RCSB:3p8y, PDBe:3p8y, PDBj:3p8y
• PDBsum: 3p8y
• PubMed: 21820443
• UniProt: Q9V228