Structure of PDB 6oet Chain C

Receptor sequence

>6oetC (length=623) Species: 10090 (Mus musculus) [Search protein sequence]

HINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTL
FLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKM
YRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGI
IDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLD
DYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHG
SQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKS
SELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTR
LEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPF
IETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLD
KHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMD
LYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITN
YFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEM
EDVLKHHWLYTSKYLQKFMNAHN

3D structure

PDB

6oet How mouse RAG recombinase avoids DNA transposition.

Chain

Resolution

3.4 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)	Binding affinity
BS01	dna	C	K388 G389 G390 R391 R393 Q394 L399 T400 R402 A403 H406 R407 Y485 K489 H501 K608 H609 G610 A720 G722 S723 Q978	K4 G5 G6 R7 R9 Q10 L15 T16 R18 A19 H22 R23 Y101 K105 H117 K224 H225 G226 A336 G338 S339 Q594
BS02	dna	C	D708 E709 S721 T933 N934 Y935	D324 E325 S337 T549 N550 Y551
BS03	dna	C	N443 L794 H795 R848 N850 G851 N852 Q962 K966 R969	N59 L410 H411 R464 N466 G467 N468 Q578 K582 R585
BS04	dna	C	N387 G390 R391 P392 R401 R402 K405 S477 C478 S479 Q480 M974 N975 R977 Q978 K989	N3 G6 R7 P8 R17 R18 K21 S93 C94 S95 Q96 M590 N591 R593 Q594 K605
BS05	dna	C	R440 N443 H445 K645 R855 P891 R894 S896 E901 E959	R56 N59 H61 K261 R471 P507 R510 S512 E517 E575
BS06	CA	C	D600 G601	D216 G217
BS07	ZN	C	C727 C730 H937 H942	C343 C346 H553 H558

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:6oet, PDBe:6oet, PDBj:6oet
PDBsum	6oet
PubMed	32015553
UniProt	P15919\|RAG1_MOUSE V(D)J recombination-activating protein 1 (Gene Name=Rag1)

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