MolNFT v1 · #143472 · protein + DNA
Zinc finger domain of WT1(-kts form) with 12+1MER oligonucleotide with 3' triplet tgt
6B0O · Wilms tumor protein: “Zinc finger domain of WT1(-kts form) with 12+1MER oligonucleotide with 3' triplet tgt”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.75). MolNFT v1 #143472 on GenesisL1: 3D structure…
- PDB
- 6B0O
- Type
- protein + DNA
- Length
- 287 residues
- Chains
- 6
- 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*AP*GP*TP*GP*T)-3'); DNA…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wilms tumor protein | protein | 119 | 36% helix, 14% strand | P19544 |
| B, E | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3') | dna | 13 | — | — |
| C, F | DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 13 | — | — |
| D | Wilms tumor protein | protein | 116 | 39% helix, 15% strand | P19544 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.75 | 0.83 | 51 | EDO |
| 2 | 220 | 0.70 | 0.87 | 30 | empty |
| 3 | 94 | 0.62 | 0.89 | 18 | empty |
| 4 | 84 | 0.62 | 0.90 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1167 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–E · 908 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 660 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 582 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–C · 576 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Compared structures
- 6B0O · Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet TGT · the same entry in another collection · chain F against F, 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 0.88
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 6B0O · PDBe 6B0O · UniProt P19544
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