Research workbench
Cryoem structure of human RAD51 on single-stranded DNA to 4.2A resolution.
Analyse Cryoem structure of human RAD51 on single-stranded DNA to 4.2A resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NP7
- Type
- protein
- Length
- 2,177 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD51 homolog 1
- UniProt
- Q06609
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | DNA repair protein RAD51 homolog 1 | protein | 311 | 42% helix, 19% strand | Q06609 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 7 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.79 | 0.90 | 55 | ANP |
| 2 | 231 | 0.77 | 0.91 | 34 | ANP |
| 3 | 231 | 0.77 | 0.91 | 34 | ANP |
| 4 | 241 | 0.76 | 0.90 | 33 | ANP |
| 5 | 230 | 0.75 | 0.90 | 35 | ANP |
Interfaces
6 interfaces between chains.
- F–G · 1891 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1882 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1875 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1875 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1874 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5NP7 · CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution. · the same entry in another collection · chain G against G, TM-score 1.00
- Q06609 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD51 homolog 1 (Q06609) · 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 Q06609
- Elsewhere: RCSB PDB 5NP7 · PDBe 5NP7 · UniProt Q06609
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