Research workbench
Crystal structure of pyrococcus furiosis RAD50 L802W mutation
Analyse Crystal structure of pyrococcus furiosis RAD50 L802W mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NCH
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair RAD50 ATPase
- UniProt
- P58301
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair RAD50 ATPase | protein | 301 | 39% helix, 32% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase | protein | 304 | 37% helix, 31% strand | P58301 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.79 | 0.81 | 90 | empty |
| 2 | 103 | 0.45 | 0.79 | 28 | empty |
| 3 | 62 | 0.41 | 0.80 | 15 | empty |
| 4 | 50 | 0.37 | 0.80 | 18 | empty |
| 5 | 62 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4NCH · Crystal Structure of Pyrococcus furiosis Rad50 L802W mutation · the same entry in another collection · chain A against A, TM-score 1.00
- P58301 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (P58301) · a predicted model of the same protein · chain B against A, TM-score 0.82
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 P58301
- Elsewhere: RCSB PDB 4NCH · PDBe 4NCH · UniProt P58301
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