Structure of PDB 6dbj Chain A

Receptor sequence

>6dbjA (length=552) Species: 7955,83333 [Search protein sequence]

FGLHPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEKE
LLPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDVPADTISRRFRY
DVALVSALKDLEEDIMEGLRERALDDSMCTSGFTVVVKESCDGMGDVSEK
HGSGPAVPEKAVRFSFTIMSISIRLEGEDDGITIFQEQKPNSELSCRPLC
LMFVDESDHETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGTG
YDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMVLHSITRSHDENLER
YEIWRKNPFSESADELRDRVKGVSAKPFMETQPTLDALHCDIGNATEFYK
IFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKMKLKPVMRMNGNYARR
LMTREAVEAVCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQL
CQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAHVPEIVERDGSIGAW
ASEGNESGNKLFRRFRKMNARQSKTFELEDILKHHWLYTSKYLQKFMEAH
KN

3D structure

PDB

6dbj DNA melting initiates the RAG catalytic pathway.

Chain

Resolution

3.0 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	S496 C497 S498 R523 M996 N997 A998 R999 K1011	S18 C19 S20 R45 M518 N519 A520 R521 K533
BS02	dna	A	K508 H520 K628 H629 G630 Q1000	K30 H42 K150 H151 G152 Q522
BS03	dna	A	A742 G744 S745 T746 K864 R870 G873 N874 E981 E984 S985 K988 R991	A264 G266 S267 T268 K386 R392 G395 N396 E503 E506 S507 K510 R513
BS04	dna	A	K667 S670 N874 R877 P913 R916 S917 T918 D923 E981	K189 S192 N396 R399 P435 R438 S439 T440 D445 E503
BS05	dna	A	D730 E731 R756 R845 R870 K953 I954 T955 N956 Y957	D252 E253 R278 R367 R392 K475 I476 T477 N478 Y479
BS06	ZN	A	C749 C752 H959 H964	C271 C274 H481 H486
BS07	CA	A	D620 G621 E984	D142 G143 E506
BS08	CA	A	D620 E684 D730	D142 E206 D252

Gene Ontology

	Molecular Function
GO:0004519	endonuclease activity
GO:0005515	protein binding
GO:0015144	carbohydrate transmembrane transporter activity
GO:0043565	sequence-specific DNA binding
GO:0046872	metal ion binding
GO:0061630	ubiquitin protein ligase activity
GO:1901982	maltose binding

	Biological Process
GO:0006974	DNA damage response
GO:0008643	carbohydrate transport
GO:0015768	maltose transport
GO:0033151	V(D)J recombination
GO:0034219	carbohydrate transmembrane transport
GO:0034289	detection of maltose stimulus
GO:0042956	maltodextrin transmembrane transport
GO:0055085	transmembrane transport
GO:0060326	cell chemotaxis

	Cellular Component
GO:0016020	membrane
GO:0030288	outer membrane-bounded periplasmic space
GO:0042597	periplasmic space
GO:0043190	ATP-binding cassette (ABC) transporter complex
GO:0055052	ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
GO:1990060	maltose transport complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:6dbj, PDBe:6dbj, PDBj:6dbj
PDBsum	6dbj
PubMed	30061602
UniProt	O13033\|RAG1_DANRE V(D)J recombination-activating protein 1 (Gene Name=rag1); P0AEX9\|MALE_ECOLI Maltose/maltodextrin-binding periplasmic protein (Gene Name=malE)

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