Research workbench
Crystal structure of MRE11:RAD50 in its ATP/ADP bound state
Analyse Crystal structure of MRE11:RAD50 in its ATP/ADP bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3THO
- Type
- protein
- Length
- 723 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable DNA double-strand break repair RAD50 ATPase; Exonuclease, putative
- UniProt
- Q9X1X1, Q9X1X0
- Ligands
- ADP, MN, MG, SO4, PO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable DNA double-strand break repair RAD50 ATPase | protein | 357 | 43% helix, 26% strand | Q9X1X1 |
| B | Exonuclease, putative | protein | 366 | 36% helix, 23% strand | Q9X1X0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.70 | 0.75 | 88 | SO4 |
| 2 | 165 | 0.57 | 0.82 | 36 | SO4 |
| 3 | 56 | 0.56 | 0.89 | 17 | empty |
| 4 | 106 | 0.51 | 0.82 | 19 | empty |
| 5 | 165 | 0.50 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3THO · Crystal structure of Mre11:Rad50 in its ATP/ADP bound state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1X1 · AlphaFold monomer V2.0 prediction for probable DNA double-strand break repair RAD50… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9X1X1
- Every structure of UniProt Q9X1X0
- Elsewhere: RCSB PDB 3THO · PDBe 3THO · UniProt Q9X1X1 · UniProt Q9X1X0
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