Structure of PDB 3pd2 Chain A Binding Site BS01

Receptor Information
>3pd2 Chain A (length=147) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDE
KNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNR
VYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEEARVE
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 chain3pd2 Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3pd2 Mechanistic insights into cognate substrate discrimination during proofreading in translation
Resolution1.86 Å
Binding residue
(original residue number in PDB)		A19 V45 P80 F81 A82 A94 F117 G118 Y119 Y120
Binding residue
(residue number reindexed from 1)		A19 V45 P80 F81 A82 A94 F117 G118 Y119 Y120
Annotation score2
Binding affinityMOAD: Kd=3.4uM
PDBbind-CN: -logKd/Ki=5.47,Kd=3.4uM
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:3pd2, PDBe:3pd2, PDBj:3pd2
PDBsum3pd2
PubMed21098258
UniProtQ9UZ14|SYT_PYRAB Threonine--tRNA ligase (Gene Name=thrS)

[Back to BioLiP]