Structure of PDB 4rrf Chain B Binding Site BS01

Receptor Information
>4rrf Chain B (length=137) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNP
EGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIES
ILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIV
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 chain4rrf 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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PDB4rrf Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		V46 Y82 A83 L89 A95 F118 G119
Binding residue
(residue number reindexed from 1)		V42 Y78 A79 L85 A91 F114 G115
Annotation score2
Binding affinityMOAD: Kd=239.2uM
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:4rrf, PDBe:4rrf, PDBj:4rrf
PDBsum4rrf
PubMed26113036
UniProtQ58597|SYT_METJA Threonine--tRNA ligase (Gene Name=thrS)

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