Structure of PDB 5k3b Chain A Binding Site BS01

Receptor Information

>5k3b Chain A (length=295) Species: 258594 (Rhodopseudomonas palustris CGA009)

DLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAP
KLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHV
HFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALK
IYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHY
RIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASG
IAQTPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA

Ligand information

• Ligand ID: R3W
• InChI: InChI=1S/C2H3ClO2/c3-1-2(4)5/h1H2,(H,4,5)
• InChIKey: FOCAUTSVDIKZOP-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: ClCC(=O)O
  OpenEye OEToolkits 1.7.0: C(C(=O)O)Cl
  CACTVS 3.370: OC(=O)CCl
• Formula: C2 H3 Cl O2
• Name: chloroacetic acid
• ChEMBL: CHEMBL14090
• ZINC: ZINC000003860254
• PDB chain: 5k3b Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k3b The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
• Resolution: 1.58 Å
• Binding residue (original residue number in PDB): N110 R111 R114 H155 W185 Y219
• Binding residue (residue number reindexed from 1): N108 R109 R112 H153 W183 Y217
• Annotation score: 2

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): F38 Q40 H107 N108 R109 D132 H153 Y217 G250 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:5k3b, PDBe:5k3b, PDBj:5k3b
• PDBsum: 5k3b
• PubMed: 28104837
• UniProt: Q6NAM1|DEHA_RHOPA Fluoroacetate dehalogenase (Gene Name=RPA1163)