Structure of PDB 6v0v Chain A

Receptor sequence

>6v0vA (length=541) Species: 10090 (Mus musculus)

GLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVL
LPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYD
SALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKPE
KAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHET
LTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEG
LEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHE
SVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYK
HPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVC
ELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFA
ELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKL
FRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

3D structure

• PDB: 6v0v Cutting antiparallel DNA strands in a single active site.
• Chain: A
• Resolution: 3.61 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	A720 G722 S723 V724 K844 I846 M847 R848	A253 G255 S256 V257 K377 I379 M380 R381
BS02	dna	A	D600 G603 D708 H795 R848 K931 T933 N934 Y935 K966 R970	D140 G143 D241 H328 R381 K464 T466 N467 Y468 K499 R503
BS03	CA	A	D600 D708	D140 D241
BS04	CA	A	D600 E962	D140 E495
BS05	ZN	A	C727 C730 H937 H942	C260 C263 H470 H475

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity
• GO:0043565 sequence-specific DNA binding
• GO:0046872 metal ion binding
• GO:0061630 ubiquitin protein ligase activity

Biological Process

• GO:0033151 V(D)J recombination

External links

• PDB: RCSB:6v0v, PDBe:6v0v, PDBj:6v0v
• PDBsum: 6v0v
• PubMed: 32015552
• UniProt: P15919|RAG1_MOUSE V(D)J recombination-activating protein 1 (Gene Name=Rag1)