Structure of PDB 4ncb Chain A Binding Site BS06

Receptor Information
>4ncb Chain A (length=676) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAG
GVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPG
ERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLD
LWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWEL
LRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPI
PHLTGLLVPVLTLEDLSLALSLPWEERRRRTREIASWIGRRLGLGTPEAV
RAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPE
FLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVL
TPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAG
LQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQ
AGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALE
ALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRD
FRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLA
DRLVKEVGRLGIRHLKEVDREKLFFV
Ligand information
Ligand IDDT
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain4ncb Chain B Residue 701 [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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PDB4ncb Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Resolution2.189 Å
Binding residue
(original residue number in PDB)		G38 R39
Binding residue
(residue number reindexed from 1)		G34 R35
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.24.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004520 DNA endonuclease activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0044355 clearance of foreign intracellular DNA

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ncb, PDBe:4ncb, PDBj:4ncb
PDBsum4ncb
PubMed24374628
UniProtQ746M7|AGO_THET2 Protein argonaute (Gene Name=ago)

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