Research workbench
Crystal structure of P. furiosus MRE11-H85S bound to a branched DNA and manganese
Analyse Crystal structure of P. furiosus MRE11-H85S bound to a branched DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DSD
- Type
- protein + DNA
- Length
- 689 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair protein MRE11; DNA (5'…
- UniProt
- Q8U1N9
- Ligands
- MN
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA double-strand break repair protein MRE11 | protein | 333 | 26% helix, 33% strand | Q8U1N9 |
| C | DNA (5'- D(*DCP*DGP*DCP*DGP*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DC P*DTP*DTP*DGP*DTP*DGP*DGP*DAP*DTP*DA)-3') | dna | 23 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.62 | 0.79 | 29 | empty |
| 2 | 191 | 0.61 | 0.83 | 29 | empty |
| 3 | 198 | 0.50 | 0.76 | 24 | empty |
| 4 | 147 | 0.44 | 0.76 | 18 | empty |
| 5 | 94 | 0.42 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 788 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 741 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 448 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3DSD · Crystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese · the same entry in another collection · chain B against B, 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 3DSD · PDBe 3DSD · UniProt Q8U1N9
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