Structure of PDB 6dbl Chain C

Receptor sequence

>6dblC (length=616) Species: 7955,83333 [Search protein sequence]

GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLA
LRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTV
KATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGL
SGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC
TSGFTVVVKESCDGMGDVSEKVPEKAVRFSFTIMSISIRLEGEDDGITIF
QEQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMESRLIISV
GGLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNM
VLHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFMETQPTL
DALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKM
KLKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDLYLQMKP
VWRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLA
HVPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELEDILKHH
WLYTSKYLQKFMEAHK

3D structure

PDB

6dbl DNA melting initiates the RAG catalytic pathway.

Chain

Resolution

5.0 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	C	G408 R410 R421 S496 C497 R523 N997 A998 R999	G1 R3 R14 S89 C90 R116 N584 A585 R586
BS02	dna	C	G409 R410 Q413 L418 R421 H501 H520 Q1000 S1001	G2 R3 Q6 L11 R14 H94 H113 Q587 S588
BS03	dna	C	R459 N462 H464 D624 D730 E731 K732 S743 R845 M869 R870 T955 N956 K988	R52 N55 H57 D217 D317 E318 K319 S330 R432 M456 R457 T542 N543 K575
BS04	dna	C	N462 K465 A742 G744 T746 M869	N55 K58 A329 G331 T333 M456
BS05	ZN	C	C749 L751 C752 H959 H964	C336 L338 C339 H546 H551
BS06	CA	C	D620 E984	D213 E571

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

View graph for
Cellular Component

External links

PDB	RCSB:6dbl, PDBe:6dbl, PDBj:6dbl
PDBsum	6dbl
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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