MolNFT v1 · #128632 · protein
Crystal structure of a human RAD51-ATP filament.
5NWL · DNA repair protein RAD51 homolog 1: “Crystal structure of a human RAD51-ATP filament.”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #128632 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NWL
- Type
- protein
- Length
- 4,207 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD51 homolog 1
- UniProt
- Q06609
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, K, L, N | DNA repair protein RAD51 homolog 1 | protein | 301 | 43% helix, 21% strand | Q06609 |
| B, I, J, M | DNA repair protein RAD51 homolog 1 | protein | 300 | 42% helix, 21% strand | Q06609 |
| D | DNA repair protein RAD51 homolog 1 | protein | 302 | 43% helix, 21% strand | Q06609 |
| F | DNA repair protein RAD51 homolog 1 | protein | 299 | 44% helix, 21% strand | Q06609 |
| H | DNA repair protein RAD51 homolog 1 | protein | 299 | 43% helix, 21% strand | Q06609 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 1111 | 0.85 | 0.86 | 103 | MG, ATP |
| 2 | 1081 | 0.84 | 0.85 | 108 | MG, ATP |
| 3 | 1072 | 0.84 | 0.85 | 102 | MG, ATP |
| 4 | 1154 | 0.83 | 0.84 | 108 | MG, ATP |
| 5 | 852 | 0.82 | 0.85 | 86 | empty |
Interfaces
15 interfaces between chains.
- L–M · 1866 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1772 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1763 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1741 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1630 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5NWL · Crystal structure of a human RAD51-ATP filament. · the same entry in another collection · chain N against N, TM-score 1.00
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 5NWL · PDBe 5NWL · UniProt Q06609
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