Structure of PDB 4ncb Chain A

Receptor sequence

>4ncbA (length=676) Species: 274 (Thermus thermophilus) [Search protein sequence]

GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAG
GVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPG
ERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLD
LWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWEL
LRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPI
PHLTGLLVPVLTLEDLSLALSLPWEERRRRTREIASWIGRRLGLGTPEAV
RAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPE
FLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVL
TPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAG
LQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQ
AGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALE
ALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRD
FRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLA
DRLVKEVGRLGIRHLKEVDREKLFFV

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	A	Y43 R59 A170 Y171 R172 I173 R192 T201 L265 T266 L267 L279 S280 L281 R286 P412 M413 W415 K422 Q433 I434 L435 N436 R446 N449 K457 E512 R513 P550 Q551 R580 G612 T613 R615 P650 R651 H657 R661 V685	Y39 R55 A166 Y167 R168 I169 R188 T197 L261 T262 L263 L270 S271 L272 R277 P403 M404 W406 K413 Q424 I425 L426 N427 R437 N440 K448 E503 R504 P541 Q542 R571 G603 T604 R606 P641 R642 H648 R652 V676
BS02	dna	A	R51 R114 G547 R548 R574 K575 S576 K618	R47 R110 G538 R539 R565 K566 S567 K609
BS03	dna	A	R51 R114 E268 K329 H445 D478 G480 G481 D546 G547 R548 R574 K575 S576 D590 V606 R608 K618 F647 A648 F649 K664 R668	R47 R110 E264 K320 H436 D469 G471 G472 D537 G538 R539 R565 K566 S567 D581 V597 R599 K609 F638 A639 F640 K655 R659
BS04	DT	A	Y197 R200 L217 P218 L223 Y226 H227 R232 I254 P255 H256	Y193 R196 L213 P214 L219 Y222 H223 R228 I250 P251 H252
BS05	MG	A	D478 D660	D469 D651
BS06	DT	A	G38 R39	G34 R35
BS07	MG	A	D478 D546	D469 D537

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

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Molecular Function

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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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