Research workbench
Crystal structure of human KLF4 zinc finger DNA binding domain in complex with nanog DNA
Analyse Crystal structure of human KLF4 zinc finger DNA binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VTX
- 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(*AP*GP*GP*GP*GP*GP*TP*GP*TP*GP*CP*C)-3'); DNA…
- UniProt
- O43474
- Ligands
- ZN, NA
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Krueppel-like factor 4 | protein | 83 | 40% helix, 12% strand | O43474 |
| B | DNA (5'-D(*AP*GP*GP*GP*GP*GP*TP*GP*TP*GP*CP*C)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*GP*GP*CP*AP*CP*AP*CP*CP*CP*CP*CP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.63 | 0.88 | 26 | empty |
| 2 | 69 | 0.33 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 814 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 551 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–C · 451 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6VTX · Crystal structure of human KLF4 zinc finger DNA binding domain in complex with NANOG DNA · the same entry in another collection · chain A against A, TM-score 1.00
- O43474 · AlphaFold monomer V2.0 prediction for krueppel-like factor 4 (O43474) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 O43474
- Elsewhere: RCSB PDB 6VTX · PDBe 6VTX · UniProt O43474
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