Structure of PDB 4rvz Chain Z Binding Site BS02

Receptor Information
>4rvz Chain Z (length=420) Species: 224325 (Archaeoglobus fulgidus DSM 4304) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTIP
YKTRGNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEE
LAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVG
AELEDFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCND
VVVCIPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDM
HLIGEEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAA
FEPTKQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNP
ICPSCGRRMESAGRGQGFRCKKCRTKADEKLREKVERELQPGFYEVPPSA
RRHLSKPLIRMNVEGRHIFR
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
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)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain4rvz Chain Z Residue 502 [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]
PDB4rvz A covalent approach for site-specific RNA labeling in Mammalian cells.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D8 D9 D11 T18 L45 G55 N56 G57 A112 V116 L117 R140 G141 I143 G144
Binding residue
(residue number reindexed from 1)		D8 D9 D11 T18 L45 G55 N56 G57 A112 V116 L117 R140 G141 I143 G144
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4rvz, PDBe:4rvz, PDBj:4rvz
PDBsum4rvz
PubMed25694369
UniProtO28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)

[Back to BioLiP]