MolNFT v1 · #107903 · protein
Rada C-terminal ATPase domain from pyrococcus furiosus bound to ADP
4UQO · DNA repair and recombination protein rada: “Rada C-terminal ATPase domain from pyrococcus furiosus bound to ADP”. X-ray diffraction, 3 ligands (ADP, NA, MG), 3 pockets (best druggability 0.31). MolNFT v1 #107903 on GenesisL1: 3D…
- PDB
- 4UQO
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair and recombination protein rada
- UniProt
- O74036
- Ligands
- ADP, NA, MG
- Pockets
- 3 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 222 | 39% helix, 26% strand | O74036 |
| B | DNA repair and recombination protein rada | protein | 223 | 38% helix, 26% strand | O74036 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.31 | 0.76 | 19 | MG |
| 2 | 51 | 0.29 | 0.76 | 13 | empty |
| 3 | 58 | 0.28 | 0.74 | 16 | ADP, MG |
Interfaces
1 interface between chains.
- A–B · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UQO · Rada C-terminal ATPase domain from pyrococcus furiosus bound to ADP · the same entry in another collection · chain A against A, TM-score 1.00
- O74036 · AlphaFold monomer V2.0 prediction for DNA repair and recombination protein rada (O74036) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O74036
- Elsewhere: RCSB PDB 4UQO · PDBe 4UQO · UniProt O74036
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