Structure of PDB 4ncb Chain B

Receptor sequence

>4ncbB (length=672) Species: 274 (Thermus thermophilus) [Search protein sequence]

GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAG
GVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPG
ERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLD
LWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWEL
LRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPIPHLTGL
LVPVLTLEDLHESLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQA
YRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRR
ALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPM
AWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVV
ALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGER
IPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAR
EGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGT
PRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLV
KEVGRLGIRHLKEVDREKLFFV

3D structure

PDB

4ncb Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

Chain

Resolution

2.189 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

3.1.24.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	B	Y43 R59 A170 Y171 R172 I173 R192 T201 L265 L267 L279 S280 L281 R286 P412 M413 W415 K422 Q433 I434 N436 R446 N449 K457 E512 R513 R580 R611 T613 P614 R615 Y642 A644 S645 P650 R651 H657 R661 V685	Y39 R55 A166 Y167 R168 I169 R188 T197 L255 L257 L266 S267 L268 R273 P399 M400 W402 K409 Q420 I421 N423 R433 N436 K444 E499 R500 R567 R598 T600 P601 R602 Y629 A631 S632 P637 R638 H644 R648 V672
BS02	dna	B	E268 S276 A278 S328 K329 W415 H445 D478 G480 G481 K575 D590 V606 R608 F610 F647 A648 F649 R668	E258 S263 A265 S315 K316 W402 H432 D465 G467 G468 K562 D577 V593 R595 F597 F634 A635 F636 R655
BS03	dna	B	P44 A47 R51 R114 G547 R574 K575 S576	P40 A43 R47 R110 G534 R561 K562 S563
BS04	DT	B	Y197 R200 W202 L217 P218 Y226 H227 R232 I254 P255 H256	Y193 R196 W198 L213 P214 Y222 H223 R228 I244 P245 H246
BS05	MG	B	D478 D660	D465 D647
BS06	MG	B	D478 D546	D465 D533

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
PDBsum	4ncb
PubMed	24374628
UniProt	Q746M7\|AGO_THET2 Protein argonaute (Gene Name=ago)

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