Structure of PDB 6dbx Chain A

Receptor sequence
>6dbxA (length=615) Species: 7955,83333 [Search protein sequence]
GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLA
LRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTV
KATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGL
SGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC
TSGFTVVVKESCDGMGDVSEKHPEKAVRFSFTIMSISIRLEGEDDGITIF
QEQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMESRLIISV
GGLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNM
VLHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFMETQPTL
DALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKM
KLKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDLYLQMKP
VWRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLA
HVPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELEDILKHH
WLYTSKYLQKFMEAH
3D structure
PDB6dbx DNA melting initiates the RAG catalytic pathway.
ChainA
Resolution4.2 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)		 Binding affinity
BS01 dna A N462 H464 V868 M869 K988 R992 N55 H57 V455 M456 K575 R579
BS02 dna A K465 S626 R870 K58 S219 R457
BS03 ZN A L751 C752 H959 H964 L338 C339 H546 H551
BS04 CA A D620 E984 D213 E571
BS05 CA A D620 E684 D730 D213 E271 D317
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:6dbx, PDBe:6dbx, PDBj:6dbx
PDBsum6dbx
PubMed30061602
UniProtO13033|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]