Research workbench
HUMRADA33F in complex with peptidic inhibitor 6
Analyse HUMRADA33F in complex with peptidic inhibitor 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XTW
- Type
- protein
- Length
- 453 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
- NZW, SO4
- Pockets
- 4 · best druggability 0.61
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 | 225 | 38% helix, 26% strand | O74036 |
| B | DNA repair and recombination protein rada | protein | 228 | 37% helix, 26% strand | O74036 |
Ligands and binding sites
- NZW · ~{N}-[2-[(2~{S})-2-[[(1~{S})-1-(4-methoxyphenyl) ethyl]carbamoyl]pyrrolidin-1-yl]-2-oxidanylidene-ethyl]quinoline-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.61 | 0.82 | 41 | empty |
| 2 | 248 | 0.55 | 0.77 | 37 | empty |
| 3 | 77 | 0.39 | 0.78 | 19 | SO4 |
| 4 | 52 | 0.33 | 0.78 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6XTW · HumRadA33F in complex with peptidic inhibitor 6 · 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 0.98
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 6XTW · PDBe 6XTW · UniProt O74036
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