MolNFT v1 · #103903 · protein + DNA
Mus musculus TDP2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and MG2+
4PUQ · Tyrosyl-DNA phosphodiesterase 2: “Mus musculus TDP2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and MG2+”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.68). MolNFT v1 #103903 on GenesisL1…
- PDB
- 4PUQ
- Type
- protein + DNA
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; DNA/RNA hybrid
- EC
- 3.1.4.-
- UniProt
- Q9JJX7
- Ligands
- MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 256 | 23% helix, 36% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 23% helix, 36% strand | Q9JJX7 |
| C, D | DNA/RNA hybrid | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains B, C, A, D
- ACT · Acetate ion · additive · chains A, C, D
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 | 733 | 0.68 | 0.76 | 56 | GOL |
| 2 | 52 | 0.31 | 0.77 | 13 | empty |
| 3 | 56 | 0.28 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 479 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 433 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 367 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- B–D · 119 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–C · 118 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4PUQ · Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and… · 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 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 4PUQ · PDBe 4PUQ · UniProt Q9JJX7
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