Structure of PDB 5zdz Chain C

Receptor sequence

>5zdzC (length=623) Species: 10090 (Mus musculus) [Search protein sequence]

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

3D structure

PDB

5zdz Cracking the DNA Code for V(D)J Recombination

Chain

Resolution

2.8 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	C	G390 R391 R393 T400 R402 R407 Y485 K489 H501 K608 H609 G610 Q978	G6 R7 R9 T16 R18 R23 Y101 K105 H117 K224 H225 G226 Q594
BS02	dna	C	D708 E709 S721 H795 R848 N934 Y935	D324 E325 S337 H411 R464 N550 Y551
BS03	dna	C	N443 M602 G722 S723 V724 L794 H795 R848 N850 G851 N852 E959 E962 K966 R969	N59 M218 G338 S339 V340 L410 H411 R464 N466 G467 N468 E575 E578 K582 R585
BS04	dna	C	N387 G389 G390 R391 P392 R401 K405 S477 C478 S479 Q480 K483 R504 N975 A976 R977 Q978 K989	N3 G5 G6 R7 P8 R17 K21 S93 C94 S95 Q96 K99 R120 N591 A592 R593 Q594 K605
BS05	dna	C	N443 H445 K645 P646 N647 S648 E649 L650 N852 R855 P891 R894 S895 S896 E901 E959	N59 H61 K261 P262 N263 S264 E265 L266 N468 R471 P507 R510 S511 S512 E517 E575
BS06	CA	C	D600 G601 E962	D216 G217 E578
BS07	ZN	C	C727 C730 H937 H942	C343 C346 H553 H558

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

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:5zdz, PDBe:5zdz, PDBj:5zdz
PDBsum	5zdz
PubMed	29628308
UniProt	P15919\|RAG1_MOUSE V(D)J recombination-activating protein 1 (Gene Name=Rag1)

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