MolNFT v1 · #3815 · protein
Structure of the DNA topoisomerase VI a subunit
1D3Y: “Structure of the DNA topoisomerase VI a subunit”. X-ray diffraction, 2 ligands (MG, NA), 5 pockets (best druggability 0.65). MolNFT v1 #3815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1D3Y
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase VI a subunit
- EC
- 5.99.1.3
- UniProt
- Q57815
- Ligands
- MG, NA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase VI a subunit (EC 5.99.1.3) | protein | 289 | 51% helix, 17% strand | Q57815 |
| B | DNA topoisomerase VI a subunit (EC 5.99.1.3) | protein | 290 | 52% helix, 17% strand | Q57815 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.65 | 0.81 | 46 | empty |
| 2 | 241 | 0.60 | 0.80 | 34 | empty |
| 3 | 284 | 0.52 | 0.75 | 47 | MG |
| 4 | 52 | 0.34 | 0.78 | 10 | empty |
| 5 | 51 | 0.23 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2148 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
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 Q57815
- Elsewhere: RCSB PDB 1D3Y · PDBe 1D3Y · UniProt Q57815
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