Structure of PDB 4kpy Chain A Binding Site BS04

Receptor Information
>4kpy Chain A (length=676) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNHLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVA
RRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDP
KDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGG
AVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRR
TWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKPI
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 chain4kpy Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4kpy Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Resolution2.406 Å
Binding residue
(original residue number in PDB)		Y197 R200 W202 L217 P218 Y226 H227 R232 P255 H256
Binding residue
(residue number reindexed from 1)		Y197 R200 W202 L217 P218 Y226 H227 R232 P251 H252
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:4kpy, PDBe:4kpy, PDBj:4kpy
PDBsum4kpy
PubMed24374628
UniProtQ746M7|AGO_THET2 Protein argonaute (Gene Name=ago)

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