Structure of PDB 3amu Chain A Binding Site BS02

Receptor Information
>3amu Chain A (length=402) Species: 2234 (Archaeoglobus fulgidus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTI
PNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEELAVK
LKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVGAELE
DFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCNDVVVC
IPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDMHLIG
EEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEPT
KQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNPICPE
SAGRGQGFADEKLREKVERELQPGFYEVPPSARRHLSKPLIRMNVEGRHI
FR
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain3amu Chain A Residue 421 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3amu Structural basis of tRNA agmatinylation essential for AUA codon decoding
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D8 D9 D11 T18 L45 I49 N56 G57 A112 L117 R140 I143 G144
Binding residue
(residue number reindexed from 1)		D9 D10 D12 T19 L46 I50 N52 G53 A108 L113 R136 I139 G140
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.4.22: tRNA(Ile)(2)-agmatinylcytidine synthase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016879 ligase activity, forming carbon-nitrogen bonds
Biological Process
GO:0002101 tRNA wobble cytosine modification
GO:0008033 tRNA processing
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3amu, PDBe:3amu, PDBj:3amu
PDBsum3amu
PubMed22002223
UniProtO28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)

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