MolNFT v2 · #158540 · protein
Crystal structure of Tdp1 catalytic domain in complex with compound XZ523
6N0O · Tyrosyl-DNA phosphodiesterase 1: “Crystal structure of Tdp1 catalytic domain in complex with compound XZ523”. X-ray diffraction at 1.943, 1 ligand (K8G), 6 pockets (best druggability 0.78). MolNFT v2 #158540 on GenesisL1: 3D…
- PDB
- 6N0O
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.943
- Source
- Homo sapiens
- Molecule
- Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- K8G
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.943 · 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
- K8G · 4-nitrobenzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.78 | 0.80 | 125 | EDO |
| 2 | 285 | 0.55 | 0.76 | 38 | K8G |
| 3 | 261 | 0.52 | 0.75 | 38 | K8G |
| 4 | 72 | 0.40 | 0.79 | 16 | empty |
| 5 | 73 | 0.40 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 671 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6N0O · Crystal structure of TDP1 catalytic domain in complex with compound XZ523 · 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 6N0O · PDBe 6N0O · UniProt Q9NUW8
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