Research workbench
Zinc finger domain of WT1(-kts form) with 13+1MER oligonucleotide with 3' triplet tgt
Analyse Zinc finger domain of WT1(-kts form) with 13+1MER oligonucleotide with 3'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0Q
- Type
- protein + DNA
- Length
- 289 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilms tumor protein; DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3'); DNA…
- UniProt
- P19544
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Wilms tumor protein | protein | 118 | 35% helix, 14% strand | P19544 |
| E, B | DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3') | dna | 13 | — | — |
| F, C | DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 13 | — | — |
| A | Wilms tumor protein | protein | 119 | 35% helix, 14% strand | P19544 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains D, A
- SO4 · Sulfate ion · ion · 8 copies · chains D, E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.72 | 0.94 | 23 | empty |
| 2 | 136 | 0.69 | 0.90 | 26 | empty |
| 3 | 93 | 0.65 | 0.91 | 18 | empty |
| 4 | 73 | 0.64 | 0.92 | 16 | empty |
| 5 | 57 | 0.32 | 0.77 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1018 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–E · 954 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–F · 631 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–F · 588 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–C · 582 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 6B0Q · Zinc finger Domain of WT1(-KTS form) with 13+1mer Oligonucleotide with 3' Triplet TGT · the same entry in another collection · chain C against C, 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 0.81
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 6B0Q · PDBe 6B0Q · UniProt P19544
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