Research workbench
Wilms tumor protein (WT1) zinc fingers in complex with formylated DNA
Analyse Wilms tumor protein (WT1) zinc fingers in complex with formylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R2Q
- Type
- protein + DNA
- Length
- 110 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilms tumor protein, isoform 4/CRA_A; DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor protein, isoform 4/CRA_A | protein | 88 | 40% helix, 14% strand | P19544 |
| B | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*TP*AP*(5FC)P*GP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 11 | — | — |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.65 | 0.94 | 16 | empty |
| 2 | 81 | 0.55 | 0.87 | 19 | empty |
| 3 | 52 | 0.33 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1010 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 503 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 491 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4R2Q · Wilms Tumor Protein (WT1) zinc fingers in complex with formylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P19544 · AlphaFold monomer V2.0 prediction for wilms tumor protein (P19544) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P19544
- Elsewhere: RCSB PDB 4R2Q · PDBe 4R2Q · UniProt P19544
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