Research workbench
DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities
Analyse DNA double-strand break repair pathway choice is directed by distinct MRE11… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O4K
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease, putative
- UniProt
- Q9X1X0
- Ligands
- 2PK, MN
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease, putative | protein | 331 | 27% helix, 28% strand | Q9X1X0 |
| B | Exonuclease, putative | protein | 321 | 28% helix, 28% strand | Q9X1X0 |
Ligands and binding sites
- 2PK · (5~{E})-2-azanylidene-5-[(4-hydroxyphenyl)methylidene]-1,3-thiazolidin-4-one · ligand · 2 copies · chains A, B
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.78 | 0.82 | 105 | 2PK, MN |
| 2 | 121 | 0.48 | 0.79 | 18 | empty |
| 3 | 58 | 0.35 | 0.78 | 17 | empty |
| 4 | 54 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 736 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4O4K · DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease… · the same entry in another collection · 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 Q9X1X0
- Elsewhere: RCSB PDB 4O4K · PDBe 4O4K · UniProt Q9X1X0
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