Research workbench
Kaiso (ZBTB33) E535A zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs)
Analyse Kaiso (ZBTB33) E535A zinc finger DNA binding domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFA
- Type
- protein + DNA
- Length
- 156 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator kaiso; DNA (5'- D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*…
- UniProt
- Q86T24
- Ligands
- ZN, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator kaiso | protein | 120 | 30% helix, 22% strand | Q86T24 |
| D | DNA (5'- D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3') | dna | 18 | — | — |
| E | DNA (5'- D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.76 | 0.94 | 25 | empty |
| 2 | 159 | 0.58 | 0.82 | 24 | empty |
| 3 | 123 | 0.41 | 0.76 | 17 | empty |
| 4 | 84 | 0.37 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- D–E · 835 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–D · 820 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–E · 748 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6DFA · Kaiso (ZBTB33) E535A zinc finger DNA binding domain in complex with the specific Kaiso… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86T24 · AlphaFold monomer V2.0 prediction for transcriptional regulator kaiso (Q86T24) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q86T24
- Elsewhere: RCSB PDB 6DFA · PDBe 6DFA · UniProt Q86T24
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.