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Crystal structure of the RAG1 nonamer-binding domain with DNA

Analyse Crystal structure of the RAG1 nonamer-binding domain with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3GNB
Type
protein + DNA
Length
96 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
V(D)J recombination-activating protein 1; 5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)…
UniProt
P15919
Pockets
1 · best druggability 0.47

Structure

x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AV(D)J recombination-activating protein 1protein6875% helix, 0% strandP15919
D5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3'dna14——
E5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3'dna14——

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11700.470.7622empty

Interfaces

3 interfaces between chains.

  • D–E · 554 Ų buried · 59 hydrogen bonds · nucleic-nucleic
  • A–E · 512 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–D · 398 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 3GNB · Crystal structure of the RAG1 nonamer-binding domain with DNA · the same entry in another collection · chain D against D, TM-score 1.00
  • P15919 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (P15919) · a predicted model of the same protein · chain A against A, TM-score 0.97

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