Structure of PDB 6dbo Chain C

Receptor sequence

>6dboC (length=542) Species: 7955,83333 [Search protein sequence]

GLHPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEKEL
LPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDVPADTISRRFRYD
VALVSALKDLEEDIMEGLRERALDDSMCTSGFTVVVKESCDGMGDVSVPE
KAVRFSFTIMSISIRLEGEDDGITIFQEQKPNSELSCRPLCLMFVDESDH
ETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGTGYDEKMVREM
EGLEASGSTYICTLCDSTRAEASQNMVLHSITRSHDENLERYEIWRKNPF
SESADELRDRVKGVSAKPFMETQPTLDALHCDIGNATEFYKIFQDEIGEV
YQKPNPSREERRRWRSTLDKQLRKKMKLKPVMRMNGNYARRLMTREAVEA
VCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQLCQYSYNSQQ
FADLLSSMFKYRYDGKITNYLHKTLAHVPEIVERDGSIGAWASEGNESGN
KLFRRFRKMNARQSKTFELEDILKHHWLYTSKYLQKFMEAHK

3D structure

PDB

6dbo DNA melting initiates the RAG catalytic pathway.

Chain

Resolution

4.4 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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	S496 N997 K1011	S17 N510 K524
BS02	dna	C	H501 R505 H520	H22 R26 H41
BS03	dna	C	D620 G623 E731 S743 K866 M869 R870 K953 T955 N956 K988 R992	D141 G144 E244 S256 K379 M382 R383 K466 T468 N469 K501 R505
BS04	dna	C	A742 G744 S745 T746 R795 K866 M869 R870	A255 G257 S258 T259 R308 K379 M382 R383
BS05	ZN	C	C749 C752 H959 H964	C262 C265 H472 H477

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:6dbo, PDBe:6dbo, PDBj:6dbo
PDBsum	6dbo
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)

[Back to BioLiP]