Structure of PDB 6d8f Chain A

Receptor sequence

>6d8fA (length=758) Species: 349102 (Cereibacter sphaeroides ATCC 17025) [Search protein sequence]

RQLVSNGFEVNLPDQVEVIVRDLPDPSKVKEERTRLMGYWFVHWFDGKLF
HLRIKAGGPNVDGEHRAIRTAEHPWLLRARLDDALEEALPKYAAVKKRPF
TFLAQKDELIDAAATAAGLSHRLLNSFKVIPRFALSPKIYEPVDGTTRVG
VFVTIGMRYDIEASLRDLLEAGIDLRGMYVVRRKRQPGERGLLGRVRAIS
DDMVQLFEETDLASVNVNDAKLEGSKENFTRCLSALLGHNYKKLLNALDD
QEAGYRTGPRFDDAVRRMGEFLAKKPIRLADNINAQVGDRIVFSNEGQAR
NVRLAPKVEYVFDRTGAKSAEYAWRGLSQFGPFDRPSFANRSPRILVVYP
SSTQGKVENFLSAFRDGMGSNYSGFSKGFVDLMGLTKVEFVMCPVEVSSA
DRNGAHTKYNSAIEDKLAGAGEVHAGIVVLFEDHARLPDDRNPYIHTKSL
LLTLGVPTQQVRMPTVLLEPKSLQYTLQNFSIATYAKLNGTPWTVNHDKA
INDELVVGMGLAELSGSRTEKRQRFVGITTVFAGDGSYLLGNVSKECEYE
GYSDAIRESMTGILRELKKRNNWRPGDTVRVVFHAHRPLKRVDVASIVFE
CTREIGSDQNIQMAFVTVSHDHPFVLIDRSERGLEAYKGSTARKGVFAPP
RGAISRVGRLTRLLAVNSPQLIKRANTPLPTPLLVSLHPDSTFKDVDYLA
EQALKFTSLSWRSTLPAATPVTIFYSERIAELLGRLKSIPNWSSANLNIK
LKWSRWFL

3D structure

PDB

6d8f Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

Chain

Resolution

2.15 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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)	Binding affinity
BS01	rna	A	P43 R151 G175 M176 R177 Y178 R204 R209 G210 L211 E242 G243 K245 R275 A454 Y463 K467 Q478 Q479 V480 R481 T484 T495 N498 F499 K506 R537 R543 R606 K609 R610 K692 S732 A737 F743 R754 L777	P24 R132 G156 M157 R158 Y159 R185 R190 G191 L192 E223 G224 K226 R256 A435 Y444 K448 Q459 Q460 V461 R462 T465 T476 N479 F480 K487 R518 R524 R587 K590 R591 K673 S713 A718 F724 R735 L758
BS02	dna	A	P45 R52 H62 W63 R97 K157 K245 E246 Y260 Y329 Y341 Y494 A531 E532 R541 H605 R606 S638 H639 D640 Y656 Q689 L690 R693 L734	P26 R33 H43 W44 R78 K138 K226 E227 Y241 Y310 Y322 Y475 A512 E513 R522 H586 R587 S619 H620 D621 Y637 Q670 L671 R674 L715

Gene Ontology

	Molecular Function
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003723	RNA binding
GO:0004520	DNA endonuclease activity
GO:0046872	metal ion binding

	Biological Process
GO:0044355	clearance of foreign intracellular DNA

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:6d8f, PDBe:6d8f, PDBj:6d8f
PDBsum	6d8f
PubMed	29996105
UniProt	A4WYU7\|AGO_CERS5 Protein argonaute (Gene Name=ago)

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