Research workbench
Zinc finger domain of WT1(+KTS form) with M342R mutation and 17+1MER oligonucleotide with triplet ggt
Analyse Zinc finger domain of WT1(+KTS form) with M342R mutation and 17+1MER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BLW
- Type
- protein + DNA
- Length
- 142 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilms tumor protein; DNA (5'- D(P*GP*CP*GP*AP*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*T)-3')…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor protein | protein | 109 | 39% helix, 11% strand | P19544 |
| B | DNA (5'- D(P*GP*CP*GP*AP*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*T)-3') | dna | 16 | — | — |
| C | DNA (5'- D(*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*TP*TP*TP*CP*GP*C)-3') | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.62 | 0.89 | 19 | EDO |
| 2 | 88 | 0.55 | 0.86 | 14 | empty |
| 3 | 81 | 0.55 | 0.86 | 16 | empty |
| 4 | 122 | 0.46 | 0.79 | 17 | empty |
| 5 | 107 | 0.37 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 969 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 733 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–C · 579 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6BLW · Zinc finger Domain of WT1(+KTS form) with M342R Mutation and 17+1mer Oligonucleotide with… · 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 0.73
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 6BLW · PDBe 6BLW · UniProt P19544
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