MolNFT v1 · #124373 · protein
Apo-structure of humanised rada-mutant HUMRADA22
5KDD · DNA repair and recombination protein rada: “Apo-structure of humanised rada-mutant HUMRADA22”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.58). MolNFT v1 #124373 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KDD
- Type
- protein
- Length
- 435 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
- SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 217 | 38% helix, 28% strand | O74036 |
| B | DNA repair and recombination protein rada | protein | 218 | 40% helix, 28% strand | O74036 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.58 | 0.89 | 21 | empty |
| 2 | 82 | 0.37 | 0.77 | 18 | SO4 |
| 3 | 59 | 0.34 | 0.77 | 18 | SO4 |
Interfaces
1 interface between chains.
- A–B · 484 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5KDD · Apo-structure of humanised RadA-mutant humRadA22 · 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 B against A, TM-score 0.99
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 5KDD · PDBe 5KDD · UniProt O74036
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