Research workbench
Mouse KLF4 ZNF1-3 (E446D) and CPG/CPG sequence DNA complex structure: form I
Analyse Mouse KLF4 ZNF1-3 (E446D) and CPG/CPG sequence DNA complex structure: form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEA
- Type
- protein + DNA
- Length
- 107 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Krueppel-like factor 4; DNA (5'-D(*GP*AP*GP*GP*CP*GP*TP*GP*GP*C)-3'); DNA…
- UniProt
- Q60793
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Krueppel-like factor 4 | protein | 87 | 39% helix, 14% strand | Q60793 |
| B | DNA (5'-D(*GP*AP*GP*GP*CP*GP*TP*GP*GP*C)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*GP*CP*CP*AP*CP*GP*CP*CP*TP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.66 | 0.86 | 28 | empty |
| 2 | 61 | 0.58 | 0.91 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 762 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 454 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 441 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5KEA · mouse Klf4 ZnF1-3 (E446D) and CpG/CpG sequence DNA complex structure: Form I · 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 0.91
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 5KEA · PDBe 5KEA · UniProt Q60793
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