MolNFT v1 · #88819 · protein
Rada C-terminal ATPase domain from pyrococcus furiosus bound to amppnp
4D6P · DNA repair and recombination protein rada: “Rada C-terminal ATPase domain from pyrococcus furiosus bound to amppnp”. X-ray diffraction, 2 ligands (ANP, MG), 4 pockets (best druggability 0.51). MolNFT v1 #88819 on GenesisL1: 3D…
- PDB
- 4D6P
- Type
- protein
- Length
- 455 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
- ANP, MG
- Pockets
- 4 · best druggability 0.51
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 | 226 | 38% helix, 26% strand | O74036 |
| B | DNA repair and recombination protein rada | protein | 229 | 37% helix, 26% strand | O74036 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.51 | 0.78 | 20 | empty |
| 2 | 73 | 0.33 | 0.75 | 20 | ANP, MG |
| 3 | 53 | 0.30 | 0.76 | 19 | ANP, MG |
| 4 | 54 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D6P · Rada C-terminal ATPase domain from pyrococcus furiosus bound to amppnp · 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 0.97
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 4D6P · PDBe 4D6P · UniProt O74036
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