Structure of PDB 6cim Chain C

Receptor sequence

>6cimC (length=602) Species: 10090 (Mus musculus)

LLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEH
RQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQ
IFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSV
DEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVV
KESCDGMGDVSEKVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELC
CKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFI
FRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHA
ENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNA
AEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNG
NFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKE
CPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDG
SIGAWNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNA
HN

3D structure

• PDB: 6cim Cracking the DNA Code for V(D)J Recombination.
• Chain: C
• Resolution: 3.6 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	L399 T400 R402 A403 Y485 K489 H501 E607 Q978 S979	L4 T5 R7 A8 Y90 K94 H106 E212 Q573 S574
BS02	dna	C	S477 C478 S479 N975 R977 D986	S82 C83 S84 N570 R572 D581
BS03	dna	C	N443 R848 M849 N965 R969	N48 R447 M448 N560 R564
BS04	dna	C	R440 A441 N443 I846 M847 R848 N850 K966	R45 A46 N48 I445 M446 R447 N449 K561
BS05	ZN	C	C727 C730 H937 H942	C326 C329 H536 H541
BS06	MN	C	D600 E662 D708	D205 E261 D307

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