MolNFT v1 · #119223 · protein
Monomeric rada in complex with fata tetrapeptide
5FPK · DNA repair and recombination protein rada: “Monomeric rada in complex with fata tetrapeptide”. X-ray diffraction, 3 ligands (ACE, NH2, PO4), 2 pockets (best druggability 0.53). MolNFT v1 #119223 on GenesisL1: 3D structure, binding…
- PDB
- 5FPK
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- 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
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 227 | 37% helix, 26% strand | O74036 |
| C | Fhtg peptide | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- NH2 · Amino group · ion · chains A, C
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.53 | 0.82 | 26 | empty |
| 2 | 85 | 0.39 | 0.77 | 20 | PO4 |
Interfaces
1 interface between chains.
- A–C · 320 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5FPK · Monomeric rada in complex with fata 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 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 5FPK · PDBe 5FPK · UniProt O74036
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