Research workbench
Cryo-electron microscopy structure of rag paired complex (with nbd, no symmetry)
Analyse Cryo-electron microscopy structure of rag paired complex (with nbd, no symmetry) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBW
- Type
- protein + DNA
- Length
- 2,168 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V(D)J recombination-activating protein 1; V(D)J recombination-activating protein 2…
- EC
- 3.1.-.-, 6.3.2.-
- UniProt
- O13033, Q1RLW7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 6.3.2.-) | protein | 622 | 47% helix, 11% strand | O13033 |
| B, D | V(D)J recombination-activating protein 2 | protein | 351 | 1% helix, 43% strand | Q1RLW7 |
| E | 12-rss signal end forward strand | dna | 34 | — | — |
| F | Nicked 12-rss intermediate reverse strand | dna | 50 | — | — |
| G | Nicked 23-rss intermediate reverse strand | dna | 61 | — | — |
| H | Nicked 23-rss intermediate forward strand | dna | 45 | — | — |
| I, J | 5'-D(P*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3' | dna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.87 | 0.91 | 78 | empty |
| 2 | 552 | 0.85 | 0.91 | 64 | empty |
| 3 | 466 | 0.85 | 0.92 | 49 | empty |
| 4 | 155 | 0.76 | 0.94 | 29 | empty |
| 5 | 711 | 0.76 | 0.81 | 67 | empty |
Interfaces
23 interfaces between chains.
- A–C · 3803 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 2045 Ų buried · 216 hydrogen bonds · nucleic-nucleic
- C–D · 1967 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1526 Ų buried · 160 hydrogen bonds · nucleic-nucleic
Compared structures
- 3JBW · Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry) · the same entry in another collection · chain J against J, TM-score 1.00
- O13033 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (O13033) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O13033
- Every structure of UniProt Q1RLW7
- Elsewhere: RCSB PDB 3JBW · PDBe 3JBW · UniProt O13033 · UniProt Q1RLW7
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