MolNFT v1 · #76437 · protein
RAD50 ABC-ATPase with adjacent coiled-coil region in complex with AMP- pnp
3QKT · DNA double-strand break repair RAD50 ATPase: “RAD50 ABC-ATPase with adjacent coiled-coil region in complex with AMP- pnp”. X-ray diffraction, 2 ligands (ANP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #76437 on GenesisL1…
- PDB
- 3QKT
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair RAD50 ATPase
- EC
- 3.6.-.-
- UniProt
- P58301
- Ligands
- ANP, MG
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA double-strand break repair RAD50 ATPase (EC 3.6.-.-) | protein | 339 | 40% helix, 30% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase (EC 3.6.-.-) | protein | 319 | 39% helix, 32% strand | P58301 |
| D | DNA double-strand break repair RAD50 ATPase (EC 3.6.-.-) | protein | 318 | 39% helix, 32% strand | P58301 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.83 | 0.84 | 154 | ANP, MG |
| 2 | 1121 | 0.80 | 0.82 | 123 | ANP, MG |
| 3 | 221 | 0.59 | 0.81 | 32 | empty |
| 4 | 227 | 0.56 | 0.79 | 50 | empty |
| 5 | 140 | 0.53 | 0.81 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1484 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1466 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 469 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3QKT · Rad50 ABC-ATPase with adjacent coiled-coil region in complex with AMP-PNP · 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 D 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 3QKT · PDBe 3QKT · UniProt P58301
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