MolNFT v1 · #143190 · protein
MRE11 dimer in complex with endonuclease inhibitor PFM04
6ASC · Nuclease sbccd subunit D: “MRE11 dimer in complex with endonuclease inhibitor PFM04”. X-ray diffraction, 2 ligands (BU7, MN), 6 pockets (best druggability 0.77). MolNFT v1 #143190 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ASC
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease sbccd subunit D
- UniProt
- Q9X1X0
- Ligands
- BU7, MN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease sbccd subunit D | protein | 331 | 26% helix, 27% strand | Q9X1X0 |
| B | Nuclease sbccd subunit D | protein | 321 | 27% helix, 28% strand | Q9X1X0 |
Ligands and binding sites
- BU7 · (5E)-3-butyl-5-[(4-hydroxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.77 | 0.84 | 66 | BU7 |
| 2 | 194 | 0.73 | 0.88 | 29 | BU7 |
| 3 | 298 | 0.58 | 0.78 | 44 | MN |
| 4 | 106 | 0.51 | 0.82 | 18 | empty |
| 5 | 112 | 0.50 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 875 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ASC · Mre11 dimer in complex with Endonuclease inhibitor PFM04 · 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 6ASC · PDBe 6ASC · UniProt Q9X1X0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.