Structure of PDB 3pd3 Chain B Binding Site BS01

Receptor Information
>3pd3 Chain B (length=143) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDE
KNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNR
VYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE
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 chain3pd3 Chain B Residue 148 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pd3 Mechanistic insights into cognate substrate discrimination during proofreading in translation
Resolution1.86 Å
Binding residue
(original residue number in PDB)		V45 P80 F81 A82 A94 F117 G118 Y119 Y120 K121
Binding residue
(residue number reindexed from 1)		V45 P80 F81 A82 A94 F117 G118 Y119 Y120 K121
Annotation score2
Binding affinityMOAD: Kd=36.2uM
PDBbind-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:3pd3, PDBe:3pd3, PDBj:3pd3
PDBsum3pd3
PubMed21098258
UniProtQ9UZ14|SYT_PYRAB Threonine--tRNA ligase (Gene Name=thrS)

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