Structure of PDB 3nem Chain B Binding Site BS01

Receptor Information
>3nem Chain B (length=438) Species: 311400 (Thermococcus kodakarensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITA
PKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNR
AETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDF
FHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMA
SGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERL
VAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIP
WGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEIC
RAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGM
PPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3nem Chain B Residue 1039 [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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PDB3nem Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation
Resolution1.89 Å
Binding residue
(original residue number in PDB)		R214 E216 H223 L224 E361 I362 S363 S364 G407 G409 R412
Binding residue
(residue number reindexed from 1)		R214 E216 H223 L224 E361 I362 S363 S364 G407 G409 R412
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R214 E216 R222 H223 E361 S364 R412
Catalytic site (residue number reindexed from 1) R214 E216 R222 H223 E361 S364 R412
Enzyme Commision number 6.1.1.12: aspartate--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004815 aspartate-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006422 aspartyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3nem, PDBe:3nem, PDBj:3nem
PDBsum3nem
PubMed9724658
UniProtQ52428|SYD_THEKO Aspartate--tRNA(Asp) ligase (Gene Name=aspS)

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