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Crystal structure of TDP1 catalytic domain in complex with zenobia fragment benzene-1,2,4-tricarboxylic acid from 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
- 6DIE
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TDP1 catalytic domain (residues 149-609)
- UniProt
- Q9NUW8
- Ligands
- GHM
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TDP1 catalytic domain (residues 149-609) | protein | 437 | 27% helix, 24% strand | Q9NUW8 |
| B | TDP1 catalytic domain (residues 149-609) | protein | 439 | 27% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- GHM · benzene-1,2,4-tricarboxylic 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.79 | 0.80 | 123 | empty |
| 2 | 262 | 0.51 | 0.75 | 32 | GHM |
| 3 | 233 | 0.49 | 0.75 | 35 | GHM |
| 4 | 90 | 0.32 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 619 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DIE · Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment… · 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 B 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 6DIE · PDBe 6DIE · UniProt Q9NUW8
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