MolNFT v1 · #109242 · protein
Crystal structure of the core RAG1/2 recombinase
4WWX · V(D)J recombination-activating protein 1: “Crystal structure of the core RAG1/2 recombinase”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #109242 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4WWX
- Type
- protein
- Length
- 1,876 residues
- Chains
- 4
- Method
- x-ray diffraction
- 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
- P15919, P21784
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 6.3.2.-) | protein | 612 | 51% helix, 12% strand | P15919 |
| X, Y | V(D)J recombination-activating protein 2 | protein | 333 | 3% helix, 44% strand | P21784 |
| E | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 6.3.2.-) | protein | 598 | 50% helix, 12% strand | P15919 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.82 | 0.86 | 70 | empty |
| 2 | 698 | 0.82 | 0.86 | 71 | empty |
| 3 | 57 | 0.70 | 0.97 | 24 | empty |
| 4 | 644 | 0.69 | 0.78 | 69 | empty |
| 5 | 548 | 0.64 | 0.76 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–E · 3100 Ų buried · 24 hydrogen bonds · protein-protein
- B–X · 2072 Ų buried · 31 hydrogen bonds · protein-protein
- E–Y · 2055 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4WWX · Crystal structure of the core RAG1/2 recombinase · the same entry in another collection · chain B against B, TM-score 1.00
- P21784 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 2 (P21784) · a predicted model of the same protein · chain X against A, TM-score 0.99
- P15919 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (P15919) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 P15919
- Every structure of UniProt P21784
- Elsewhere: RCSB PDB 4WWX · PDBe 4WWX · UniProt P15919 · UniProt P21784
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.