Research workbench
Crystal structure of TDP1 catalytic domain in complex with zenobia fragment ZT1982 (single soak)
Analyse Crystal structure of TDP1 catalytic domain in complex with zenobia fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJD
- 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
- GJP
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 438 | 27% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- GJP · 4-hydroxyquinoline-3-carboxylic 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
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 | 438 | 0.73 | 0.83 | 46 | empty |
| 2 | 302 | 0.67 | 0.82 | 51 | EDO |
| 3 | 252 | 0.52 | 0.76 | 36 | GJP |
| 4 | 236 | 0.51 | 0.75 | 35 | GJP |
| 5 | 96 | 0.48 | 0.81 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 676 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6DJD · Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982… · 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 6DJD · PDBe 6DJD · UniProt Q9NUW8
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