MolNFT v1 · #91036 · protein + DNA
Crystal structure of TDP2 from danio rerio complexed with a single strand DNA
4F1H · DNA (5'-D(P*TP*GP*CP*AP*G)-3'): “Crystal structure of TDP2 from danio rerio complexed with a single strand DNA”. X-ray diffraction, 2 ligands (MG, PO4), 3 pockets (best druggability 0.76). MolNFT v1 #91036 on GenesisL1: 3D…
- PDB
- 4F1H
- Type
- protein + DNA
- Length
- 506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*GP*CP*AP*G)-3'); Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- Q5XJA0
- Ligands
- MG, PO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(P*TP*GP*CP*AP*G)-3') | dna | 5 | — | — |
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 250 | 23% helix, 36% strand | Q5XJA0 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 251 | 22% helix, 36% strand | Q5XJA0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C, A
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.76 | 0.83 | 60 | empty |
| 2 | 341 | 0.63 | 0.79 | 45 | empty |
| 3 | 58 | 0.27 | 0.74 | 15 | GOL |
Interfaces
3 interfaces between chains.
- C–A · 680 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 582 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 185 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4F1H · Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q5XJA0 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q5XJA0) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q5XJA0
- Elsewhere: RCSB PDB 4F1H · PDBe 4F1H · UniProt Q5XJA0
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