Structure of PDB 4rra Chain A Binding Site BS01

Receptor Information
>4rra Chain A (length=136) Species: 272557 (Aeropyrum pernix K1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQT
VMYAASDIASHSSRLKVTTVILYPYAHLSSRLAKPMAAHKRLIELEGALR
TKFPGHVHRAPFGWYKSFSIACKGHPLAELSRSFTE
Ligand information
Ligand IDA3T
InChIInChI=1S/C14H21N7O5/c1-5(23)7(15)13(25)20-8-6(2-22)26-14(10(8)24)21-4-19-9-11(16)17-3-18-12(9)21/h3-8,10,14,22-24H,2,15H2,1H3,(H,20,25)(H2,16,17,18)/t5-,6-,7+,8-,10-,14-/m1/s1
InChIKeyJYCQZCJEBNTMCV-JHJLZTHQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C(C(=O)NC1C(OC(C1O)n2cnc3c2ncnc3N)CO)N)O
OpenEye OEToolkits 1.7.0C[C@H]([C@@H](C(=O)N[C@@H]1[C@H](O[C@H]([C@@H]1O)n2cnc3c2ncnc3N)CO)N)O
CACTVS 3.370C[CH](O)[CH](N)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO)n2cnc3c(N)ncnc23
CACTVS 3.370C[C@@H](O)[C@H](N)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)C(O)C
FormulaC14 H21 N7 O5
Name3'-deoxy-3'-(L-threonylamino)adenosine
ChEMBL
DrugBank
ZINCZINC000058631685
PDB chain4rra Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4rra Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		V42 P74 Y75 L82 A88 F112 G113 W114 Y115
Binding residue
(residue number reindexed from 1)		V42 P74 Y75 L82 A88 F112 G113 W114 Y115
Annotation score2
Binding affinityMOAD: Kd=13.4uM
PDBbind-CN: -logKd/Ki=4.87,Kd=13.4uM
Enzymatic activity
Enzyme Commision number 6.1.1.3: threonine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4rra, PDBe:4rra, PDBj:4rra
PDBsum4rra
PubMed26113036
UniProtQ9YFY3|SYTE_AERPE Threonine--tRNA ligase editing subunit (Gene Name=thrS2)

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