MolNFT v1 · #143475 · protein + DNA
Zinc finger domain of WT1(-kts form) with M342R mutation and 14+1MER oligonucleotide with 3' triplet tgg
6B0R · Wilms tumor protein: “Zinc finger domain of WT1(-kts form) with M342R mutation and 14+1MER oligonucleotide with 3' triplet tgg”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.74). MolNFT v1 #143475 on GenesisL1…
- PDB
- 6B0R
- Type
- protein + DNA
- Length
- 294 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*GP*GP*TP*TP*A)- 3'); DNA…
- UniProt
- P19544
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Wilms tumor protein | protein | 117 | 40% helix, 15% strand | P19544 |
| E, B | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)- 3') | dna | 15 | — | — |
| F | DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 14 | — | — |
| A | Wilms tumor protein | protein | 118 | 40% helix, 14% strand | P19544 |
| C | DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 15 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains D, 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.74 | 0.83 | 56 | EDO |
| 2 | 138 | 0.59 | 0.85 | 23 | empty |
| 3 | 66 | 0.55 | 0.88 | 13 | empty |
| 4 | 78 | 0.55 | 0.87 | 16 | empty |
| 5 | 77 | 0.53 | 0.86 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1277 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–E · 1267 Ų buried · 32 hydrogen bonds · protein-nucleic
- D–F · 710 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 671 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 646 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Compared structures
- 6B0R · Zinc finger Domain of WT1(-KTS form) with M342R Mutation and 14+1mer Oligonucleotide with… · the same entry in another collection · chain E against E, TM-score 1.00
- P19544 · AlphaFold monomer V2.0 prediction for wilms tumor protein (P19544) · a predicted model of the same protein · chain D against A, TM-score 0.87
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 6B0R · PDBe 6B0R · UniProt P19544
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