MolNFT v1 · #68201 · protein + DNA
Cryo-electron microscopy structure of rag paired complex (C2 symmetry)
3JBY · V(D)J recombination-activating protein 1: “Cryo-electron microscopy structure of rag paired complex (C2 symmetry)”. Electron microscopy, 2 ligands (CA, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #68201 on GenesisL1: 3D…
- PDB
- 3JBY
- Type
- protein + DNA
- Length
- 1,926 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
- CA, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 29% helix, 25% 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 | 550 | 47% helix, 13% strand | O13033 |
| B, D | V(D)J recombination-activating protein 2 | protein | 351 | 1% helix, 43% strand | Q1RLW7 |
| E, H | 5'-D(P*CP*AP*CP*AP*GP*TP*GP*CP*TP*AP*CP*AP*GP*AP*C)-3' | dna | 15 | — | — |
| F, G | Rss intermediate reverse strand | dna | 31 | — | — |
| I, J | '-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
- CA · Calcium ion · metal · 4 copies · chains A, G, I, C, F, J
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.87 | 0.89 | 106 | empty |
| 2 | 544 | 0.84 | 0.89 | 52 | empty |
| 3 | 403 | 0.82 | 0.91 | 53 | empty |
| 4 | 299 | 0.78 | 0.90 | 42 | empty |
| 5 | 204 | 0.76 | 0.91 | 32 | empty |
Interfaces
23 interfaces between chains.
- C–D · 1956 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1898 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1849 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1008 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–F · 958 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3JBY · Cryo-electron microscopy structure of RAG Paired Complex (C2 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 0.99
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 3JBY · PDBe 3JBY · UniProt O13033 · UniProt Q1RLW7
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