Structure of PDB 6cik Chain A

Receptor sequence

>6cikA (length=607) Species: 10090 (Mus musculus)

HLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNE
HRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGR
QIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASS
VDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVV
VKESCDGMGDVSEKVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSEL
CCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKF
IFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSH
AENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGN
AAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMN
GNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAK
ECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERD
GSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQ
KFMNAHN

3D structure

• PDB: 6cik Cracking the DNA Code for V(D)J Recombination.
• Chain: A
• Resolution: 3.15 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	A	M602 M849 N965 R969	M208 M449 N565 R569
BS02	dna	A	A441 I846 R848 N850	A47 I446 R448 N450
BS03	dna	A	T400 Y485 K489 Q495 H501 Q978	T6 Y91 K95 Q101 H107 Q578
BS04	dna	A	S477 C478 S479 R504 N975 R977	S83 C84 S85 R110 N575 R577
BS05	ZN	A	C727 C730 H937 H942	C327 C330 H537 H542
BS06	MN	A	D600 E662 D708	D206 E262 D308

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