MolNFT v1 · #122389 · protein
Mouse TDP2 protein, apo state with variable DNA-binding grasp conformations
5INM · Tyrosyl-DNA phosphodiesterase 2: “Mouse TDP2 protein, apo state with variable DNA-binding grasp conformations”. X-ray diffraction, 2 ligands (MG, SO4), 15 pockets (best druggability 0.76). MolNFT v1 #122389 on GenesisL1: 3D…
- PDB
- 5INM
- Type
- protein
- Length
- 1,208 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
- MG, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 246 | 22% helix, 37% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 237 | 24% helix, 38% strand | Q9JJX7 |
| C | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 231 | 24% helix, 38% strand | Q9JJX7 |
| D | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 248 | 21% helix, 37% strand | Q9JJX7 |
| E | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 246 | 23% helix, 37% strand | Q9JJX7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, E
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.76 | 0.84 | 52 | MG |
| 2 | 690 | 0.73 | 0.79 | 89 | empty |
| 3 | 506 | 0.70 | 0.80 | 45 | empty |
| 4 | 429 | 0.63 | 0.77 | 48 | empty |
| 5 | 249 | 0.56 | 0.78 | 34 | empty |
Interfaces
7 interfaces between chains.
- C–D · 578 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 366 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5INM · Mouse Tdp2 protein, apo state with variable DNA-binding grasp conformations · 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 C 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 5INM · PDBe 5INM · UniProt Q9JJX7
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