Structure of PDB 8jpx Chain B

Receptor sequence

>8jpxB (length=770) Species: 186497 (Pyrococcus furiosus DSM 3638) [Search protein sequence]

MKAIVVINLVKINKKIIPDKIYVYRLFNDPEEELQKEGYSIYRLAYENVG
IVIDPENLIIATTKELEYEGEFIPEGEISFSELRNDYQSKLVLRLLKENG
IGEYELSKLLRKFRKPKTFGDYKVIPSVEMSVIKHDEDFYLVIHIIHQIQ
SMKTLWELVNKDPKELEEFLMTHKENLMLKDIASPLKTVYKPCFEEYTKK
PKLDHNQEIVKYWYNYHIERYWNTPEAKLEFYRKFGQVDLKQPAILAKFA
SKIKKNKNYKIYLLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELL
ENILAEVDSDIIDKSLSEIEVEKIAQELENKIRVRDDKGNSVPISQLNVQ
KSQLLLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDSGLLADIQNFA
TNEFRELVKSMYYSLAKKYNSLAKKARSTNEIGLPFLDFRGKEKVITEDL
NSDKGIIEVVEQVSSFMKGKELGLAFIAARNKLSSEKFEEIKRRLFNLNV
ISQVVNEDTLKNKRDKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDYRFN
YDYIIGIDVAPMKRSEGYIGGSAVMFDSQGYIRKIVPIKIGEQRGESVDM
NEFFKEMVDKFKEFNIKLDNKKILLLRDGRITNNEEEGLKYISEMFDIEV
VTMDVIKNHPVRAFANMKMYFNLGGAIYLIPHKLKQAKGTPIPIKLAKKR
IIKNGKVEKQSITRQDVLDIFILTRLNYGSISADMRLPAPVHYAHKFANA
IRNEWKIKEEFLAEGFLYFV

3D structure

PDB

8jpx Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonautre

Chain

Resolution

2.9 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	Y42 P55 E56 H147 M178 S251 K252 T289 K290 F488 K492 Q503 V504 V505 N506 K513 V526 N529 Q533 R630 N633 H682 G689 T690 P691 I692 N727 G729 M735 R736	Y42 P55 E56 H147 M178 S251 K252 T289 K290 F488 K492 Q503 V504 V505 N506 K513 V526 N529 Q533 R630 N633 H682 G689 T690 P691 I692 N727 G729 M735 R736
BS02	dna	B	Y42 Y46 N273 A274 K283 S352 Q353 Y364 F525 H528 D558 P561 I656 K657 N658 K685 I731 S732 H745	Y42 Y46 N273 A274 K283 S352 Q353 Y364 F525 H528 D558 P561 I656 K657 N658 K685 I731 S732 H745
BS03	dna	B	N402 R405 K409 F436 D438 F439 R440	N402 R405 K409 F436 D438 F439 R440
BS04	MG	B	D558 H745	D558 H745
BS05	MG	B	Q533 V770	Q533 V770

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:0006259	DNA metabolic process
GO:0044355	clearance of foreign intracellular DNA

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:8jpx, PDBe:8jpx, PDBj:8jpx
PDBsum	8jpx
PubMed	38295801
UniProt	Q8U3D2\|AGO_PYRFU Protein argonaute (Gene Name=ago)

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