Research workbench
Humanised monomeric rada in complex with whta tetrapeptide
Analyse Humanised monomeric rada in complex with whta tetrapeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOW
- Type
- protein
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair and recombination protein rada; Whta peptide
- UniProt
- O74036
- Ligands
- ACE, NH2, PO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 222 | 39% helix, 27% strand | O74036 |
| C | DNA repair and recombination protein rada | protein | 217 | 40% helix, 27% strand | O74036 |
| E, F | Whta peptide | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, E, C, F
- NH2 · Amino group · ion · 2 copies · chains A, E, C, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
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 | 99 | 0.55 | 0.84 | 20 | empty |
| 2 | 60 | 0.38 | 0.80 | 16 | PO4 |
| 3 | 82 | 0.36 | 0.76 | 17 | PO4 |
Interfaces
3 interfaces between chains.
- C–F · 345 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 340 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5FOW · Humanised monomeric rada in complex with whta tetrapeptide · 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 C 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 5FOW · PDBe 5FOW · UniProt O74036
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