Structure of PDB 4rr7 Chain A Binding Site BS01

Receptor Information
>4rr7 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 IDA3S
InChIInChI=1S/C13H19N7O5/c14-5(1-21)12(24)19-7-6(2-22)25-13(9(7)23)20-4-18-8-10(15)16-3-17-11(8)20/h3-7,9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,7+,9+,13+/m0/s1
InChIKeyITDKSTILAWHDJI-AYEBZEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)NC(=O)C(CO)N)O)N
ACDLabs 10.04O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)[C@H](CO)N)O)N
CACTVS 3.341N[C@@H](CO)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23
CACTVS 3.341N[CH](CO)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO)n2cnc3c(N)ncnc23
FormulaC13 H19 N7 O5
NameSERINE-3'-AMINOADENOSINE;
N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE
ChEMBL
DrugBankDB04024
ZINCZINC000016051527
PDB chain4rr7 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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PDB4rr7 Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		V42 Y75 A76 H77 A88 F112 G113 W114 K116
Binding residue
(residue number reindexed from 1)		V42 Y75 A76 H77 A88 F112 G113 W114 K116
Annotation score2
Binding affinityMOAD: Kd=1uM
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:4rr7, PDBe:4rr7, PDBj:4rr7
PDBsum4rr7
PubMed26113036
UniProtQ9YFY3|SYTE_AERPE Threonine--tRNA ligase editing subunit (Gene Name=thrS2)

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