Structure of PDB 3ko7 Chain C Binding Site BS01

Receptor Information
>3ko7 Chain C (length=151) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVVIQRVKGAILSVRLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCL
NLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPN
EALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI
N
Ligand information
Ligand IDDLY
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1
InChIKeyKDXKERNSBIXSRK-RXMQYKEDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCC[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCCN
CACTVS 3.341NCCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.5.0C(CCN)CC(C(=O)O)N
OpenEye OEToolkits 1.5.0C(CCN)C[C@H](C(=O)O)N
FormulaC6 H14 N2 O2
NameD-LYSINE
ChEMBLCHEMBL319497
DrugBankDB03252
ZINCZINC000001532731
PDB chain3ko7 Chain C Residue 165 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ko7 Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase
Resolution2.21 Å
Binding residue
(original residue number in PDB)		N66 W72
Binding residue
(residue number reindexed from 1)		N56 W62
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Q88 F89 T90
Catalytic site (residue number reindexed from 1) Q78 F79 T80
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:3ko7, PDBe:3ko7, PDBj:3ko7
PDBsum3ko7
PubMed20007323
UniProtQ8IIS0|DTD_PLAF7 D-aminoacyl-tRNA deacylase (Gene Name=DTD)

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