Structure of PDB 6cil Chain A

Receptor sequence

>6cilA (length=585) Species: 10090 (Mus musculus)

LRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQG
RGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAE
KVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRF
RYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSE
KEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDH
ETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREV
EGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPY
HESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEV
YKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDA
VCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQR
FAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGQSGNKLFRRFR
KMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHN

3D structure

• PDB: 6cil Cracking the DNA Code for V(D)J Recombination.
• Chain: A
• 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	A	R848 M849 Q962 N965 R969	R433 M434 Q540 N543 R547
BS02	dna	A	R440 A441 H445 I846 M847 R848 N850 N852	R33 A34 H38 I431 M432 R433 N435 N437
BS03	dna	A	Y485 K489 Q495 H501 E607 Q978	Y78 K82 Q88 H94 E200 Q556
BS04	dna	A	S477 C478 S479 N975 R977	S70 C71 S72 N553 R555
BS05	ZN	A	C727 C730 H937 H942	C312 C315 H522 H527
BS06	MN	A	D600 E662 D708	D193 E247 D293

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)