MolNFT v1 · #119200 · protein
Humanised monomeric rada in complex with fhtg tetrapeptide
5FOV · DNA repair and recombination protein rada: “Humanised monomeric rada in complex with fhtg tetrapeptide”. X-ray diffraction, 3 ligands (ACE, NH2, PO4), 4 pockets (best druggability 0.57). MolNFT v1 #119200 on GenesisL1: 3D structure…
- PDB
- 5FOV
- Type
- protein
- Length
- 455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair and recombination protein rada; Fhtg peptide
- UniProt
- O74036
- Ligands
- ACE, NH2, PO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 227 | 38% helix, 26% strand | O74036 |
| C | DNA repair and recombination protein rada | protein | 220 | 39% helix, 26% strand | O74036 |
| E, F | Fhtg 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
- GOL · Glycerol · additive · chains C
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 | 149 | 0.57 | 0.82 | 27 | empty |
| 2 | 175 | 0.40 | 0.72 | 20 | empty |
| 3 | 88 | 0.37 | 0.76 | 19 | PO4 |
| 4 | 68 | 0.32 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–F · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 315 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 131 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5FOV · Humanised monomeric rada in complex with fhtg 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 0.97
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 5FOV · PDBe 5FOV · UniProt O74036
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