MolNFT v1 · #167742 · protein + DNA
Crystal structure of human KLF4 zinc finger DNA binding domain in complex with nanog DNA
6VTX · Krueppel-like factor 4: “Crystal structure of human KLF4 zinc finger DNA binding domain in complex with nanog DNA”. X-ray diffraction, 2 ligands (ZN, NA), 2 pockets (best druggability 0.63). MolNFT v1 #167742 on GenesisL1: 3D…
- 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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