Structure of PDB 6oem Chain A

Receptor sequence

>6oemA (length=606) Species: 10090 (Mus musculus) [Search protein sequence]

TRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQAD
ELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQP
LHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYP
VDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESC
DGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSE
LCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFK
FIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRS
HAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIG
NAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRM
NGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPA
KECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIER
DGSIGAWANQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKF
MNAHNA

3D structure

PDB

6oem Cutting antiparallel DNA strands in a single active site.

Chain

Resolution

3.6 Å

3D
structure

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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)
BS01	dna	A	P499 H501 Q978 S979 K980	P100 H102 Q576 S577 K578
BS02	dna	A	A441 I846 R848 N850 N852 Q962	A42 I447 R449 N451 N453 Q560
BS03	dna	A	R446 M602 R848 N965 R969	R47 M203 R449 N563 R567
BS04	dna	A	K405 S477 C478 S479 R504 N975 A976 R977 Q978	K6 S78 C79 S80 R105 N573 A574 R575 Q576
BS05	MG	A	D600 D708	D201 D309
BS06	ZN	A	C727 H937 H942	C328 H538 H543

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0004519	endonuclease activity
GO:0004842	ubiquitin-protein transferase activity
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0016740	transferase activity
GO:0042393	histone binding
GO:0042802	identical protein binding
GO:0042803	protein homodimerization activity
GO:0043565	sequence-specific DNA binding
GO:0046872	metal ion binding
GO:0061630	ubiquitin protein ligase activity

	Biological Process
GO:0002250	adaptive immune response
GO:0002331	pre-B cell allelic exclusion
GO:0006310	DNA recombination
GO:0006325	chromatin organization
GO:0008542	visual learning
GO:0030183	B cell differentiation
GO:0033077	T cell differentiation in thymus
GO:0033151	V(D)J recombination
GO:0043029	T cell homeostasis
GO:0045580	regulation of T cell differentiation
GO:0045582	positive regulation of T cell differentiation
GO:0048538	thymus development
GO:0051865	protein autoubiquitination
GO:0070233	negative regulation of T cell apoptotic process
GO:0070244	negative regulation of thymocyte apoptotic process
GO:2000822	regulation of behavioral fear response

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

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

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