Research workbench
Crystal structure of the zinc finger domain of KLF4 bound to its target DNA
Analyse Crystal structure of the zinc finger domain of KLF4 bound to its target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WBS
- Type
- protein + DNA
- Length
- 101 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Krueppel-like factor 4; 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'; 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'
- UniProt
- Q60793
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Krueppel-like factor 4 | protein | 87 | 36% helix, 14% strand | Q60793 |
| F | 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3' | dna | 7 | — | — |
| G | 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3' | dna | 7 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.27 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–F · 489 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–G · 326 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–G · 254 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 2WBS · Crystal structure of the zinc finger domain of Klf4 bound to its target DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q60793 · AlphaFold monomer V2.0 prediction for krueppel-like factor 4 (Q60793) · a predicted model of the same protein · chain A against A, TM-score 0.66
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 Q60793
- Elsewhere: RCSB PDB 2WBS · PDBe 2WBS · UniProt Q60793
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