Structure of PDB 5k3e Chain A Binding Site BS01

Receptor Information

>5k3e Chain A (length=295) Species: 258594 (Rhodopseudomonas palustris CGA009)

LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPK
LAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVH
FALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKI
YHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYR
IAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGI
AQSTPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA

Ligand information

• Ligand ID: GOA
• InChI: InChI=1S/C2H4O3/c3-1-2(4)5/h3H,1H2,(H,4,5)
• InChIKey: AEMRFAOFKBGASW-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)CO
  OpenEye OEToolkits 1.7.0: C(C(=O)O)O
  CACTVS 3.370: OCC(O)=O
• Formula: C2 H4 O3
• Name: GLYCOLIC ACID;
  HYDROXYACETIC ACID;
  HYDROXYETHANOIC ACID
• ChEMBL: CHEMBL252557
• DrugBank: DB03085
• ZINC: ZINC000004658557
• PDB chain: 5k3e Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k3e The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
• Resolution: 1.54 Å
• Binding residue (original residue number in PDB): N110 R111 R114 W156 Y219 H280
• Binding residue (residue number reindexed from 1): N107 R108 R111 W153 Y216 H275
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): F40 Q42 H109 N110 R111 D134 H155 Y219 G252 H280
• Catalytic site (residue number reindexed from 1): F37 Q39 H106 N107 R108 D131 H152 Y216 G249 H275
• Enzyme Commision number: 3.8.1.3: haloacetate dehalogenase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016787 hydrolase activity
• GO:0018785 haloacetate dehalogenase activity

External links

• PDB: RCSB:5k3e, PDBe:5k3e, PDBj:5k3e
• PDBsum: 5k3e
• PubMed: 28104837
• UniProt: Q6NAM1|DEHA_RHOPA Fluoroacetate dehalogenase (Gene Name=RPA1163)