Structure of PDB 3ko5 Chain B Binding Site BS01

Receptor Information
>3ko5 Chain B (length=154) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVVIQRVKGAILSVRKKELEIISEIKNGLICFLGIHKNDTWEDALYIIR
KCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAK
EPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDT
HDIN
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3ko5 Chain B Residue 165 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ko5 Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase
Resolution2.09 Å
Binding residue
(original residue number in PDB)		F89 A106 K107 P109
Binding residue
(residue number reindexed from 1)		F82 A99 K100 P102
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q88 F89 T90
Catalytic site (residue number reindexed from 1) Q81 F82 T83
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ko5, PDBe:3ko5, PDBj:3ko5
PDBsum3ko5
PubMed20007323
UniProtQ8IIS0|DTD_PLAF7 D-aminoacyl-tRNA deacylase (Gene Name=DTD)

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