MolNFT v1 · #100947 · protein
Crystal structure of pyrococcus furiosis RAD50 R797G mutation
4NCK · DNA double-strand break repair RAD50 ATPase: “Crystal structure of pyrococcus furiosis RAD50 R797G mutation”. X-ray diffraction, 3 ligands (MG, SO4, CL), 6 pockets (best druggability 0.55). MolNFT v1 #100947 on GenesisL1: 3D…
- PDB
- 4NCK
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair RAD50 ATPase
- UniProt
- P58301
- Ligands
- MG, SO4, CL
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair RAD50 ATPase | protein | 313 | 41% helix, 30% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase | protein | 309 | 42% helix, 30% strand | P58301 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.55 | 0.76 | 37 | empty |
| 2 | 66 | 0.39 | 0.78 | 11 | empty |
| 3 | 54 | 0.38 | 0.80 | 16 | empty |
| 4 | 66 | 0.35 | 0.77 | 12 | empty |
| 5 | 58 | 0.33 | 0.76 | 12 | MG |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NCK · Crystal Structure of Pyrococcus furiosis Rad50 R797G mutation · the same entry in another collection · chain A against A, TM-score 1.00
- P58301 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (P58301) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P58301
- Elsewhere: RCSB PDB 4NCK · PDBe 4NCK · UniProt P58301
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.