MolNFT v1 · #105363 · protein + DNA
Wilms tumor protein (WT1) zinc fingers in complex with hydroxymethylated DNA
4R2P · Wilms tumor protein, isoform 4/CRA_A: “Wilms tumor protein (WT1) zinc fingers in complex with hydroxymethylated DNA”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.62). MolNFT v1 #105363 on GenesisL1: 3D…
- PDB
- 4R2P
- Type
- protein + DNA
- Length
- 111 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*(5HC)P*GP*T)-3')…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor protein, isoform 4/CRA_A | protein | 89 | 40% helix, 13% strand | P19544 |
| B | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.62 | 0.91 | 17 | empty |
| 2 | 59 | 0.31 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 952 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 614 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 490 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4R2P · Wilms Tumor Protein (WT1) zinc fingers in complex with hydroxymethylated 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 4R2P · PDBe 4R2P · UniProt P19544
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