Research workbench
Crystal structure of MRE11-RAD50 bound to ATP S
Analyse Crystal structure of MRE11-RAD50 bound to ATP S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AV0
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair protein MRE11; DNA double-strand break repair RAD50 ATPase
- UniProt
- Q58719, Q58718
- Ligands
- AGS, MG, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair protein MRE11 | protein | 369 | 35% helix, 22% strand | Q58719 |
| B | DNA double-strand break repair RAD50 ATPase | protein | 365 | 39% helix, 22% strand | Q58718 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.80 | 0.82 | 89 | SO4, IPA |
| 2 | 74 | 0.72 | 0.96 | 23 | empty |
| 3 | 153 | 0.51 | 0.79 | 28 | empty |
| 4 | 125 | 0.47 | 0.79 | 19 | empty |
| 5 | 91 | 0.45 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2429 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3AV0 · Crystal structure of Mre11-Rad50 bound to ATP S · the same entry in another collection · chain A against A, TM-score 1.00
- Q58719 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair protein MRE11… · a predicted model of the same protein · chain A against A, TM-score 0.83
- Q58718 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (Q58718) · a predicted model of the same protein · chain B against A, TM-score 0.73
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 Q58719
- Every structure of UniProt Q58718
- Elsewhere: RCSB PDB 3AV0 · PDBe 3AV0 · UniProt Q58719 · UniProt Q58718
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