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Crystal structure of pyrococcus furiosis RAD50 R805E mutation with ADP beryllium flouride
Analyse Crystal structure of pyrococcus furiosis RAD50 R805E mutation with ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NCJ
- Type
- protein
- Length
- 1,263 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair RAD50 ATPase
- UniProt
- P58301
- Ligands
- ADP, BEF, MG
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair RAD50 ATPase | protein | 311 | 38% helix, 31% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase | protein | 311 | 36% helix, 34% strand | P58301 |
| C | DNA double-strand break repair RAD50 ATPase | protein | 320 | 40% helix, 31% strand | P58301 |
| D | DNA double-strand break repair RAD50 ATPase | protein | 321 | 41% helix, 31% strand | P58301 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.82 | 0.84 | 125 | ADP, BEF, MG |
| 2 | 1058 | 0.81 | 0.83 | 128 | ADP, BEF, MG |
| 3 | 317 | 0.55 | 0.75 | 32 | empty |
| 4 | 183 | 0.53 | 0.79 | 42 | empty |
| 5 | 132 | 0.49 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1495 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1461 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NCJ · Crystal Structure of Pyrococcus furiosis Rad50 R805E mutation with ADP Beryllium Flouride · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.99
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 4NCJ · PDBe 4NCJ · UniProt P58301
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