Structure of PDB 8sjd Chain B

Receptor sequence

>8sjdB (length=477) Species: 7370 (Musca domestica)

RELKTVSADCKKEAIEKCAQWVVRDCRPFSAVSGSGFIDMIKFFIKVGAE
YGEHVNVEELLPSPITLSRKVTSDAKEKKALISREIKSAVEKDGASATID
LWTDNYIKRNFLGVTLHYHENNELRDLILGLKSLDFERSTAENIYKKLKA
IFSQFNVEDLSSIKFVTDRGANVVKSLANNIRINCSSHLLSNVLENSFEE
TPELNMPILACKNIVKYFKKANLQHRLRSSLKSECPTRWNSTYTMLRSIL
DNWESVIQILSEAGETQRIVHINKSIIQTMVNILDGFERIFKELQTCSSP
SLCFVVPSILKVKEICSPDVGDVADIAKLKVNIIKNVRIIWEENLSIWHY
TAFFFYPPALHMQQEKVAQIKEFCLSKMEDLELIPVCPSDEFEFYRKEIV
ILSEDFKVMEWWNLNSKKYPKLSKLALSLLSIPASSAASERTFSLAGNII
TEKRNRIGQQTVDSLLFLNSFYKNFCK

3D structure

• PDB: 8sjd Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding.
• Chain: B
• Resolution: 5.1 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	dna	B	L181 N190 R218 T220 A221 A251 N252 K255 S310 P316 T317 R318	L101 N110 R138 T140 A141 A171 N172 K175 S230 P236 T237 R238
BS02	dna	B	F109 S110 R573	F29 S30 R441
BS03	dna	B	S143 T146 E584 N587	S63 T66 E452 N455
BS04	dna	B	D248 R249 H268 N272	D168 R169 H188 N192
BS05	dna	B	R107 K585 R586 I589 G590 T593	R27 K453 R454 I457 G458 T461

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0046872 metal ion binding
• GO:0046983 protein dimerization activity

Biological Process

• GO:0006357 regulation of transcription by RNA polymerase II

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:8sjd, PDBe:8sjd, PDBj:8sjd
• PDBsum: 8sjd
• PubMed: 37491363
• UniProt: Q25438