Structure of PDB 6xny Chain A

Receptor sequence

>6xnyA (length=550) Species: 10090 (Mus musculus) [Search protein sequence]

GSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEK
VLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFR
YDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEK
HGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSVLCCKPLCLM
LADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYD
EKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYE
VWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIF
QLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMMMNGNFARKLM
TQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQ
YSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWAS
EGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

3D structure

PDB

6xny Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase.

Chain

Resolution

2.9 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	Y485 K489 Q495 P499 H501 S606 K608 H609 G610 A720 G722 S723 R773 M847 Q978	Y27 K31 Q37 P41 H43 S148 K150 H151 G152 A262 G264 S265 R315 M389 Q520
BS02	dna	A	G603 K618 L794 H795 I798 M848 N850 G851 N852 R855 E959 E962 S963 K966 R969	G145 K160 L336 H337 I340 M390 N392 G393 N394 R397 E501 E504 S505 K508 R511
BS03	dna	A	D708 E709 K710 S721 G722 R734 H795 E803 R927 K931 T933 N934 Y935	D250 E251 K252 S263 G264 R276 H337 E345 R469 K473 T475 N476 Y477
BS04	dna	A	K645 S648 L650 N852 R855 P891 R894 S895 E901 E959	K187 S190 L192 N394 R397 P433 R436 S437 E443 E501
BS05	dna	A	S477 C478 S479 Q480 K483 R504 M974 N975 A976 R977 D986 K989	S19 C20 S21 Q22 K25 R46 M516 N517 A518 R519 D528 K531
BS06	MG	A	G601 E962	G143 E504
BS07	MG	A	E662 D708	E204 D250
BS08	ZN	A	C727 C730 H937 H942	C269 C272 H479 H484

Gene Ontology

	Molecular Function
GO:0004519	endonuclease activity
GO:0043565	sequence-specific DNA binding
GO:0046872	metal ion 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:6xny, PDBe:6xny, PDBj:6xny
PDBsum	6xny
PubMed	32945578
UniProt	P15919\|RAG1_MOUSE V(D)J recombination-activating protein 1 (Gene Name=Rag1)

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