Research workbench
Wilms tumor protein (WT1) ZNF2-4Q369R in complex with carboxylated DNA
Analyse Wilms tumor protein (WT1) ZNF2-4Q369R in complex with carboxylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KL7
- Type
- protein + DNA
- Length
- 109 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilms tumor protein; DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3'); DNA…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor protein | protein | 87 | 40% helix, 14% strand | P19544 |
| B | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*TP*AP*(5CM)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, B, C
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 | 89 | 0.53 | 0.85 | 17 | EDO |
| 2 | 50 | 0.32 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 968 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 592 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 483 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5KL7 · Wilms Tumor Protein (WT1) ZnF2-4Q369R in complex with carboxylated 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 5KL7 · PDBe 5KL7 · UniProt P19544
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