Structure of PDB 6agg Chain Z Binding Site BS02

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 IDAG2
InChIInChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChIKeyQYPPJABKJHAVHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCCNC(N)=N
ACDLabs 10.04[N@H]=C(N)NCCCCN
OpenEye OEToolkits 1.5.0C(CCNC(=N)N)CN
FormulaC5 H14 N4
NameAGMATINE;
(4-AMINOBUTYL)GUANIDINE
ChEMBLCHEMBL58343
DrugBankDB08838
ZINCZINC000001532560
PDB chain6agg Chain Z Residue 503 [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)		D193 N194 V203 C204 G215 R217
Binding residue
(residue number reindexed from 1)		D193 N194 V203 C204 G215 R217
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.07,Kd=85uM
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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