MolNFT v1 · #122390 · protein
Mouse TDP2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp conformations
5INN · Tyrosyl-DNA phosphodiesterase 2: “Mouse TDP2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp conformations”. X-ray diffraction, 2 ligands (SO4, CL), 13 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 5INN
- Type
- protein
- Length
- 1,182 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- Q9JJX7
- Ligands
- SO4, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 242 | 22% helix, 36% strand | Q9JJX7 |
| B, E | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 233 | 20% helix, 39% strand | Q9JJX7 |
| C | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 229 | 23% helix, 38% strand | Q9JJX7 |
| D | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 245 | 18% helix, 37% strand | Q9JJX7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, E
- CL · Chloride ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.78 | 0.80 | 86 | empty |
| 2 | 558 | 0.73 | 0.81 | 57 | empty |
| 3 | 620 | 0.73 | 0.80 | 55 | empty |
| 4 | 403 | 0.63 | 0.78 | 43 | empty |
| 5 | 297 | 0.60 | 0.78 | 39 | empty |
Interfaces
7 interfaces between chains.
- C–D · 668 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 529 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 380 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 356 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5INN · Mouse Tdp2 D358N protein, apo state with increased disorder amongst variable DNA-binding… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9JJX7 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) · 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 Q9JJX7
- Elsewhere: RCSB PDB 5INN · PDBe 5INN · UniProt Q9JJX7
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