Structure of PDB 6cil Chain C

Receptor sequence

>6cilC (length=589) Species: 10090 (Mus musculus)

LSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARRQAD
ELEAIGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHAL
RNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTI
AKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMG
DVSEKEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLAD
ESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKL
VREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWR
SNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLE
IGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQE
TVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSF
NSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGQSGNKLF
RRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHN

3D structure

• PDB: 6cil Cracking the DNA Code for V(D)J Recombination.
• Chain: C
• Resolution: 4.15 Å

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.
  3.1.-.-

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	C	T400 A403 Y485 H501 E607 Q978	T4 A7 Y82 H98 E204 Q560
BS02	dna	C	S477 C478 S479 N975 A976 R977	S74 C75 S76 N557 A558 R559
BS03	dna	C	M602 M849 N965 R969	M199 M438 N547 R551
BS04	dna	C	R440 I846 M847 N850 N852	R44 I435 M436 N439 N441
BS05	ZN	C	C727 C730 H937 H942	C316 C319 H526 H531
BS06	MN	C	D600 D708	D197 D297

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity
• GO:0043565 sequence-specific DNA binding
• GO:0061630 ubiquitin protein ligase activity

Biological Process

• GO:0033151 V(D)J recombination

External links

• PDB: RCSB:6cil, PDBe:6cil, PDBj:6cil
• PDBsum: 6cil
• PubMed: 29628308
• UniProt: P15919|RAG1_MOUSE V(D)J recombination-activating protein 1 (Gene Name=Rag1)