MolNFT v1 · #171749 · protein
Pyrococcus furiosus RAD50 coiled coils in rod configuration
6ZFF · DNA double-strand break repair RAD50 ATPase: “Pyrococcus furiosus RAD50 coiled coils in rod configuration”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.62). MolNFT v1 #171749 on GenesisL1: 3D structure, binding…
- PDB
- 6ZFF
- Type
- protein
- Length
- 250 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
- ZN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair RAD50 ATPase | protein | 126 | 83% helix, 0% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase | protein | 124 | 84% helix, 0% strand | P58301 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.62 | 0.75 | 47 | empty |
| 2 | 293 | 0.52 | 0.74 | 30 | empty |
| 3 | 68 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 774 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ZFF · Pyrococcus furiosus Rad50 coiled coils in rod configuration · 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 0.83
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 6ZFF · PDBe 6ZFF · UniProt P58301
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