Research workbench
Crystal structure of TDP1 catalytic domain in complex with compound XZ578
Analyse Crystal structure of TDP1 catalytic domain in complex with compound XZ578 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N19
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- K8V
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 438 | 28% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- K8V · 4-[(4-carboxybutanoyl)amino]benzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.79 | 0.80 | 94 | empty |
| 2 | 226 | 0.58 | 0.80 | 37 | empty |
| 3 | 301 | 0.56 | 0.76 | 34 | K8V |
| 4 | 273 | 0.54 | 0.76 | 38 | K8V |
| 5 | 65 | 0.38 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 677 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6N19 · Crystal structure of Tdp1 catalytic domain in complex with compound XZ578 · 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 Q9NUW8
- Elsewhere: RCSB PDB 6N19 · PDBe 6N19 · UniProt Q9NUW8
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