Research workbench
Crystal structure of P. furiosus MRE11 with manganese and damp
Analyse Crystal structure of P. furiosus MRE11 with manganese and damp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1II7
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRE11 nuclease
- UniProt
- Q8U1N9
- Ligands
- DA, MN, SO4, PO4
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRE11 nuclease | protein | 333 | 26% helix, 32% strand | Q8U1N9 |
| B | MRE11 nuclease | protein | 332 | 27% helix, 31% strand | Q8U1N9 |
Ligands and binding sites
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.49 | 0.76 | 25 | empty |
| 2 | 127 | 0.41 | 0.75 | 22 | empty |
| 3 | 122 | 0.41 | 0.75 | 18 | PO4 |
| 4 | 90 | 0.38 | 0.76 | 18 | MN, DA |
| 5 | 89 | 0.36 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1II7 · Crystal structure of P. furiosus Mre11 with manganese and dAMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U1N9 · 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 1.00
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 Q8U1N9
- Elsewhere: RCSB PDB 1II7 · PDBe 1II7 · UniProt Q8U1N9
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