Structure of PDB 6dbt Chain A

Receptor sequence

>6dbtA (length=614) Species: 7955,83333 [Search protein sequence]

GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLA
LRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTV
KATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGL
SGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC
TSGFTVVVKESCDGMGDVSEKPEKAVRFSFTIMSISIRLEGEDDGITIFQ
EQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMESRLIISVG
GLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMV
LHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFMETQPTLD
ALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKMK
LKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDLYLQMKPV
WRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAH
VPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELEDILKHHW
LYTSKYLQKFMEAH

3D structure

PDB

6dbt DNA melting initiates the RAG catalytic pathway.

Chain

Resolution

4.3 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	V868 N872 R992	V454 N458 R578
BS02	dna	A	K465 S626 R870	K58 S219 R456
BS03	dna	A	R410 R420 K424 R428 K431 S496 C497 N997 A998 R999 D1008	R3 R13 K17 R21 K24 S89 C90 N583 A584 R585 D594
BS04	dna	A	G408 G409 R410 R421 A422 R426 K628	G1 G2 R3 R14 A15 R19 K221
BS05	ZN	A	C752 H959 H964	C338 H545 H550
BS06	CA	A	D620 E984	D213 E570

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:6dbt, PDBe:6dbt, PDBj:6dbt
PDBsum	6dbt
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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