Structure of PDB 6dbi Chain A

Receptor sequence

>6dbiA (length=622) Species: 7955,83333 [Search protein sequence]

GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLA
LRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTV
KATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGL
SGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC
TSGFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTIMSISIRLEGED
DGITIFQEQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMES
RLIISVGGLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRA
EASQNMVLHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFM
ETQPTLDALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDK
QLRKKMKLKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDL
YLQMKPVWRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNY
LHKTLAHVPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELE
DILKHHWLYTSKYLQKFMEAHK

3D structure

PDB

6dbi DNA melting initiates the RAG catalytic pathway.

Chain

Resolution

3.4 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	R459 A460 K667 S670 P913 T918 E981	R52 A53 K260 S263 P506 T511 E574
BS02	dna	A	E463 H464 K465 L816 R870 N872 E981 E984 K988	E56 H57 K58 L409 R463 N465 E574 E577 K581
BS03	dna	A	G408 R410 R412 L418 R426 H520 K628 H629 G630 Q1000	G1 R3 R5 L11 R19 H113 K221 H222 G223 Q593
BS04	dna	A	R410 P411 R420 S496 C497 S498 R523 M996 N997 R999 K1011	R3 P4 R13 S89 C90 S91 R116 M589 N590 R592 K604
BS05	dna	A	D730 E731 S743 R870 T955 N956 Y957	D323 E324 S336 R463 T548 N549 Y550
BS06	ZN	A	C749 C752 H959 H964	C342 C345 H552 H557

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

View graph for
Biological Process

View graph for
Cellular Component

External links

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