Research workbench
MRE11 RAD50 binding domain in complex with RAD50 and AMP-pnp
Analyse MRE11 RAD50 binding domain in complex with RAD50 and AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QKU
- Type
- protein
- Length
- 692 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair RAD50 ATPase; DNA double-strand break repair protein MRE11
- EC
- 3.6.-.-, 3.1.-.-
- UniProt
- P58301, Q8U1N9
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair RAD50 ATPase (EC 3.6.-.-) | protein | 359 | 42% helix, 26% strand | P58301 |
| B | DNA double-strand break repair RAD50 ATPase (EC 3.6.-.-) | protein | 301 | 32% helix, 32% strand | P58301 |
| C | DNA double-strand break repair protein MRE11 (EC 3.1.-.-) | protein | 32 | 59% helix, 0% strand | Q8U1N9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.72 | 0.76 | 82 | empty |
| 2 | 124 | 0.42 | 0.76 | 17 | empty |
| 3 | 85 | 0.37 | 0.76 | 18 | empty |
| 4 | 51 | 0.34 | 0.78 | 14 | empty |
| 5 | 72 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 953 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3QKU · Mre11 Rad50 binding domain in complex with Rad50 and 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 B against A, TM-score 0.98
- Q8U1N9 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair protein MRE11… · a predicted model of the same protein · chain C 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 P58301
- Every structure of UniProt Q8U1N9
- Elsewhere: RCSB PDB 3QKU · PDBe 3QKU · UniProt P58301 · UniProt Q8U1N9
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