Structure of PDB 3jby Chain D

Receptor sequence
>3jbyD (length=351) Species: 7955 (Danio rerio) [Search protein sequence]
MSLQPLTAVNCGSLVQPGFSLLDLEGDVYLFGQKGWPKRSCPTGIFGVRI
KKGELKLRAISFSNNSSYLPPLRCPAIAHFEAQDGKPECYLIHGGRTPNN
ELSSSLYMLSVDSRGCNRKVTLRCEEKELVGDVPSARYGHTLSVINSRGK
TACVLFGGRSYMPPTERTTQNWNSVVDCPPQVYLIDLEFGCCTAHTLPEL
TDGQSFHVALARQDCVYFLGGHILSSDCRPSRLIRLHVELLLGSPVLTCT
ILHEGLTITSAIASPIGYHEYIIFGGYQSETQKRMECTYVGLDDVGVHME
SREPPQWTSEISHSRTWFGGSLGKGTALVAIPSEGNPTPPEAYHFYQVSF
Q
3D structure
PDB3jby Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.
ChainD
Resolution3.7 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 ?
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 D K38 R39 S40 R118 K38 R39 S40 R118
BS02 dna D N10 R49 K56 R58 N10 R49 K56 R58
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding
GO:0008270 zinc ion binding
GO:0035064 methylated histone binding
GO:0035091 phosphatidylinositol binding
GO:0043325 phosphatidylinositol-3,4-bisphosphate binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding
GO:1990238 double-stranded DNA endonuclease activity
Biological Process
GO:0006310 DNA recombination
GO:0006325 chromatin organization
GO:0030098 lymphocyte differentiation
GO:0030183 B cell differentiation
GO:0030217 T cell differentiation
GO:0033077 T cell differentiation in thymus
GO:0033151 V(D)J recombination
GO:0033152 immunoglobulin V(D)J recombination
GO:0048534 hematopoietic or lymphoid organ development
GO:0048538 thymus development
GO:0065004 protein-DNA complex assembly
Cellular Component
GO:0005634 nucleus
GO:0097519 DNA recombinase complex
GO:1905347 endodeoxyribonuclease complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jby, PDBe:3jby, PDBj:3jby
PDBsum3jby
PubMed26548953
UniProtO13034|RAG2_DANRE V(D)J recombination-activating protein 2 (Gene Name=rag2)

[Back to BioLiP]