MolNFT v1 · #10156 · protein
Crystal structure of the P. furiosus RAD50 ATPase domain
1II8 · RAD50 ABC-ATPase: “Crystal structure of the P. furiosus RAD50 ATPase domain”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.43). MolNFT v1 #10156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1II8
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAD50 ABC-ATPase
- UniProt
- P58301
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAD50 ABC-ATPase | protein | 195 | 41% helix, 27% strand | P58301 |
| B | RAD50 ABC-ATPase | protein | 174 | 54% helix, 22% strand | P58301 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.43 | 0.77 | 19 | empty |
| 2 | 64 | 0.36 | 0.78 | 15 | empty |
| 3 | 71 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3608 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 1II8 · Crystal structure of the P. furiosus Rad50 ATPase domain · 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 0.71
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 1II8 · PDBe 1II8 · UniProt P58301
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