Research workbench
Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA
Analyse Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JP9
- Type
- protein + DNA
- Length
- 153 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*D C)-3')…
- UniProt
- Q4VXV4
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.63
Structure
solution nmr · 3 distinct chains · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*D C)-3') | dna | 17 | — | — |
| C | DNA (5'- D(P*DGP*DCP*DGP*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*D G)-3') | dna | 17 | — | — |
| A | Wilms tumor 1 | protein | 119 | 38% helix, 12% strand | Q4VXV4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
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 | 82 | 0.63 | 0.90 | 25 | empty |
| 2 | 68 | 0.37 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1132 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–A · 990 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 792 Ų buried · 84 hydrogen bonds · nucleic-nucleic
Compared structures
- 2JP9 · Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA · the same entry in another collection · chain B against B, 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 Q4VXV4
- Elsewhere: RCSB PDB 2JP9 · PDBe 2JP9 · UniProt Q4VXV4
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