Structure of PDB 5xp8 Chain A

Receptor sequence

>5xp8A (length=678) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence]

NHLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVAR
RAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPK
DPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGA
VLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRT
WELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPR
KPIPHLTGLLVPVLTLEDLHALSLPWEERRRRTREIASWIGRRLGLGTPE
AVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGW
PEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVL
VLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAK
AGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPE
AQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALA
LEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVH
RDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLH
LADRLVKEVGRLGIRHLKEVDREKLFFV

3D structure

PDB

5xp8 Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.

Chain

Resolution

3.1 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 A170 Y171 R172 I173 T201 L265 L267 R286 M413 W415 K422 Q433 I434 L435 N436 H445 R446 N449 K457 E512 R513 R580 V606 R611 T613 P614 R615 S645 F647 A648 P650 R651 R661 V685	Y42 A169 Y170 R171 I172 T200 L264 L266 R279 M406 W408 K415 Q426 I427 L428 N429 H438 R439 N442 K450 E505 R506 R573 V599 R604 T606 P607 R608 S638 F640 A641 P643 R644 R654 V678
BS02	dna	A	R51 R114 E268 S328 K329 H445 D478 G480 G481 D546 K575 D590 V606 R608 F647 F649 K664 R668	R50 R113 E267 S321 K322 H438 D471 G473 G474 D539 K568 D583 V599 R601 F640 F642 K657 R661
BS03	dna	A	Y197 L217 L223 Y226 H227 R232 I254 P255	Y196 L216 L222 Y225 H226 R231 I253 P254
BS04	MG	A	D478 D660	D471 D653
BS05	MG	A	D478 D546	D471 D539

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:5xp8, PDBe:5xp8, PDBj:5xp8
PDBsum	5xp8
PubMed	28911094
UniProt	Q746M7\|AGO_THET2 Protein argonaute (Gene Name=ago)

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