Structure of PDB 6oer Chain A

Receptor sequence

>6oerA (length=608) Species: 10090 (Mus musculus) [Search protein sequence]

RRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADE
LEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPL
HALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPV
DTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCD
GMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSEL
CCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKF
IFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSH
AENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGN
AAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMN
GNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAK
ECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERD
GSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQ
KFMNAHNA

3D structure

PDB

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

Chain

Resolution

3.29 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	A720 G722 V724 M847 R848 N850 H1006	A320 G322 V324 M447 R448 N450 H606
BS02	dna	A	R440 A441 H445 E709 S721 R734 H795 R848 K931 T933 N934 Y935 K966	R40 A41 H45 E309 S321 R334 H395 R448 K531 T533 N534 Y535 K566
BS03	dna	A	R402 A403 H406 K489 P499 H501 H609 Q978	R2 A3 H6 K89 P99 H101 H209 Q578
BS04	dna	A	R401 S477 C478 R504 N975 A976 R977	R1 S77 C78 R104 N575 A576 R577
BS05	ZN	A	C727 H937 H942	C327 H537 H542
BS06	CA	A	D600 D708	D200 D308
BS07	CA	A	D600 Q962	D200 Q562

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

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Biological Process

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Cellular Component

External links

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

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