Structure of PDB 5zdz Chain A

Receptor sequence

>5zdzA (length=618) Species: 10090 (Mus musculus) [Search protein sequence]

RPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALR
ARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKA
ITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSG
LASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGP
FTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKV
FEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLE
MGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQN
LVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPS
IDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKR
MNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMK
PVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTL
AHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKH
HWLYTSKYLQKFMNAHNA

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	A	N443 G722 S723 V724 L794 H795 R848 G851 N852 R855 E959 S963 K966 R969	N53 G332 S333 V334 L404 H405 R458 G461 N462 R465 E569 S573 K576 R579
BS02	dna	A	D708 E709 S721 H795 R848 K931 N934 Y935	D318 E319 S331 H405 R458 K541 N544 Y545
BS03	dna	A	R391 R393 Q394 T400 R402 A403 R407 Y485 K489 Q495 H501 K608 H609 G610 Q978	R1 R3 Q4 T10 R12 A13 R17 Y95 K99 Q105 H111 K218 H219 G220 Q588
BS04	dna	A	R440 K645 N647 S648 L650 N852 R855 P891 R894 S895 S896 E901 E959	R50 K255 N257 S258 L260 N462 R465 P501 R504 S505 S506 E511 E569
BS05	dna	A	P392 R401 K405 S477 C478 S479 Q480 K483 R504 M974 N975 A976 R977 K989	P2 R11 K15 S87 C88 S89 Q90 K93 R114 M584 N585 A586 R587 K599
BS06	CA	A	D600 E962	D210 E572
BS07	ZN	A	C727 C730 H937 H942	C337 C340 H547 H552

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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