Structure of PDB 8iby Chain C

Receptor sequence

>8ibyC (length=793) Species: 7091 (Bombyx mori)

TSRQKRRAEYARVQELYKKCRSRAAAEVIDGACGGVGHSLEEMETYWRPI
LERVSDAPGPTPEALHALGRTQLWKPISVEEIKASRFDWRTSPGPDGIRS
GQWRAVPVHLKAEMFNAWMARGEIPEILRQCRTVFVPKVERPGGPGEYRP
ISIASIPLRHFHSILARRLLACCPPDARQRGFICADGTLENSAVLDAVLG
DSRKKLRECHVAVLDFAKAFDTVSHEALVELLRLRGMPEQFCGYIAHLYD
TASTTLAVNNEMSSPVKVGRGVRQGDPLSPILFNVVMDLILASLPERVGY
RLEMELVSALAYAYDLVLLAGSKVGMQESISAVDCVGRQMGLRLNCRKSA
VLSMIPDGHRKKHHYLTERTFNIGGKPLRQVSCVERWRYLGVDFEASGCV
TLEHSISSALNNISRAPLKPQQRLEILRAHLIPRFQHGFVLGNISDDRLR
MLDVQIRKAVGQWLRLPADVPKAYYHAAVQDGGLAIPSVRATIPDLIVRR
FGGLDSSPWSVARAAAKSDKIRKKLRWAWKQLRRFSRVDSTTQRPSVRLF
WREHLHASVDGRELRESTRTPTSTKWIRERCAQITGRDFVQFVHTHINAL
PSRIRGSRGRRGGGESSLTCRAGCKVRETTAHILQQCHRTHGGRILRHNK
IVSFVAKAMEENKWTVELEPRLRTSVGLRKPAIIASRDGVGVIVDVQVVS
GQRSLDELHREKRNKYGNHGELVELVAGRLGLPKAECVRATSCTISWRGV
WSLTSYKELRSIIGLREPTLQIVPILALRGSHMNWTRFNQMTS

3D structure

• PDB: 8iby Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon.
• Chain: C
• Resolution: 3.47 Å

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	C	S306 R310 R311 Y314 I354 R357 G460 R661 C697 E699 H718 K733 D761 R764 M765 K786 K837 A896 R901 G956 N963 K971 E974 R1093 M1097	S2 R6 R7 Y10 I50 R53 G146 R347 C383 E385 H404 K419 D447 R450 M451 K472 K523 A582 R587 G642 N649 K657 E660 R779 M783
BS02	ZN	C	C938 H946	C624 H632

Gene Ontology

Molecular Function

• GO:0003964 RNA-directed DNA polymerase activity

Biological Process

• GO:0006278 RNA-templated DNA biosynthetic process
• GO:0071897 DNA biosynthetic process

External links

• PDB: RCSB:8iby, PDBe:8iby, PDBj:8iby
• PDBsum: 8iby
• PubMed: 37301196
• UniProt: V9H052