Structure of PDB 4yrk Chain B Binding Site BS01

Receptor Information

>4yrk Chain B (length=411) Species: 353153 (Trypanosoma cruzi strain CL Brener)

MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEEL
YIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAK
WYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSS
KDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMEEEVEAQLAVLGL
EPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWV
LFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIP
CAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRL
RDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLR
RGFAVPLDRLV

Ligand information

• Ligand ID: HIS
• InChI: InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/p+1/t5-/m0/s1
• InChIKey: HNDVDQJCIGZPNO-YFKPBYRVSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: c1c([nH+]c[nH]1)CC(C(=O)O)N
  CACTVS 3.341: N[CH](Cc1c[nH]c[nH+]1)C(O)=O
  CACTVS 3.341: N[C@@H](Cc1c[nH]c[nH+]1)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)Cc1cnc[nH+]1
  OpenEye OEToolkits 1.5.0: c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N
• Formula: C6 H10 N3 O2
• Name: HISTIDINE
• PDB chain: 4yrk Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yrk A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): T128 D174 L316 Y318 Y319 G359 F360 G361
• Binding residue (residue number reindexed from 1): T81 D122 L260 Y262 Y263 G303 F304 G305
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 6.1.1.21: histidine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0004821 histidine-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity

Biological Process

• GO:0006427 histidyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4yrk, PDBe:4yrk, PDBj:4yrk
• PDBsum: 4yrk
• PubMed: 26249349
• UniProt: Q4DA54