Research workbench
Mouse TDP2 catalytic domain bound to SUMO2
Analyse Mouse TDP2 catalytic domain bound to SUMO2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVQ
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; Small ubiquitin-related modifier 2
- EC
- 3.1.4.-
- UniProt
- Q9JJX7, P61957
- Ligands
- CA
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 253 | 21% helix, 38% strand | Q9JJX7 |
| B | Small ubiquitin-related modifier 2 | protein | 75 | 16% helix, 33% strand | P61957 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.52 | 0.78 | 20 | empty |
| 2 | 118 | 0.39 | 0.75 | 23 | CA |
| 3 | 70 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 819 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5TVQ · Mouse Tdp2 catalytic domain bound to SUMO2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JJX7 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61957 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 2 (P61957) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9JJX7
- Every structure of UniProt P61957
- Elsewhere: RCSB PDB 5TVQ · PDBe 5TVQ · UniProt Q9JJX7 · UniProt P61957
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.