MolNFT v1 · #146503 · protein
Crystal structure of TDP1 catalytic domain in complex with compound XZ515
6DJH · Tyrosyl-DNA phosphodiesterase 1: “Crystal structure of TDP1 catalytic domain in complex with compound XZ515”. X-ray diffraction, 1 ligand (GNM), 7 pockets (best druggability 0.78). MolNFT v1 #146503 on GenesisL1: 3D structure…
- PDB
- 6DJH
- Type
- protein
- Length
- 875 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
- GNM
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 438 | 27% helix, 24% strand | Q9NUW8 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 437 | 28% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- GNM · 8-bromo-4-oxo-1,4-dihydroquinoline-3-carboxylic 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.78 | 0.80 | 103 | empty |
| 2 | 259 | 0.52 | 0.76 | 34 | GNM |
| 3 | 248 | 0.51 | 0.75 | 35 | GNM |
| 4 | 73 | 0.39 | 0.79 | 14 | empty |
| 5 | 59 | 0.35 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DJH · Crystal structure of Tdp1 catalytic domain in complex with compound XZ515 · 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 6DJH · PDBe 6DJH · UniProt Q9NUW8
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