Structure of PDB 4rrr Chain B Binding Site BS01

Receptor Information
>4rrr Chain B (length=142) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDE
KNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNR
VYQGLKERGFNVGKAPFGYYMAFKISCKGHPLAELSRTIVPE
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 chain4rrr Chain B 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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PDB4rrr Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		L20 V45 P80 F81 A82 L88 A94 F117 G118 Y119 Y120
Binding residue
(residue number reindexed from 1)		L20 V45 P80 F81 A82 L88 A94 F117 G118 Y119 Y120
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=4.44,Kd=36.2uM
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:4rrr, PDBe:4rrr, PDBj:4rrr
PDBsum4rrr
PubMed26113036
UniProtQ9UZ14|SYT_PYRAB Threonine--tRNA ligase (Gene Name=thrS)

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