Research workbench
Structure of KLF4 zinc finger DNA binding domain in complex with methylated DNA
Analyse Structure of KLF4 zinc finger DNA binding domain in complex with methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M9E
- Type
- protein + DNA
- Length
- 105 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*(5CM)P*GP*TP*GP*GP*C)-3'); DNA…
- UniProt
- Q60793
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.65
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 | 85 | 39% helix, 14% strand | Q60793 |
| B | DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A, C
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 | 239 | 0.65 | 0.83 | 46 | ACT |
| 2 | 73 | 0.64 | 0.92 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 637 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 452 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–C · 423 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4M9E · Structure of Klf4 zinc finger DNA binding domain in complex with methylated 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 0.91
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 4M9E · PDBe 4M9E · UniProt Q60793
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