Structure of PDB 6agg Chain Z Binding Site BS01

Receptor Information
>6agg 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 chain6agg Chain Z Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6agg Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
Resolution2.706 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6agg, PDBe:6agg, PDBj:6agg
PDBsum6agg
PubMed30121296
UniProtO28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)

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