Research workbench
Crystal structure of TDP1 catalytic domain in complex with compound XZ503
Analyse Crystal structure of TDP1 catalytic domain in complex with compound XZ503 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJG
- 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
- GNJ
- Pockets
- 7 · best druggability 0.77
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
- GNJ · 4-hydroxy-8-sulfoquinoline-3-carboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.77 | 0.80 | 97 | EDO |
| 2 | 252 | 0.62 | 0.81 | 47 | empty |
| 3 | 266 | 0.53 | 0.76 | 34 | GNJ |
| 4 | 253 | 0.51 | 0.75 | 37 | GNJ |
| 5 | 60 | 0.38 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6DJG · Crystal structure of Tdp1 catalytic domain in complex with compound XZ503 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NUW8 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 1 (Q9NUW8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6DJG · PDBe 6DJG · UniProt Q9NUW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.