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
- 2PRT
- Type
- protein + DNA
- Length
- 141 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilms tumor 1; DNA (5'- D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3'); DNA (5'…
- UniProt
- Q4VXV4
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor 1 | protein | 115 | 37% helix, 16% strand | Q4VXV4 |
| B | DNA (5'- D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3') | dna | 12 | — | — |
| C | DNA (5'- D(*CP*AP*GP*AP*CP*GP*CP*CP*CP*CP*CP*GP*CP*G)-3') | dna | 14 | — | — |
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
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 | 104 | 0.67 | 0.91 | 23 | empty |
| 2 | 90 | 0.53 | 0.84 | 16 | empty |
| 3 | 232 | 0.49 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 898 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 666 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 587 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Compared structures
- 2PRT · Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA · the same entry in another collection · chain A 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 Q4VXV4
- Elsewhere: RCSB PDB 2PRT · PDBe 2PRT · UniProt Q4VXV4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.