Research workbench
Crystal structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA
Analyse Crystal structure of kaiso zinc finger DNA binding domain in complex with kaiso… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F6M
- Type
- protein + DNA
- Length
- 154 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator kaiso; DNA (5'- D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*…
- UniProt
- Q86T24
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator kaiso | protein | 116 | 31% helix, 22% strand | Q86T24 |
| D | DNA (5'- D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3') | dna | 19 | — | — |
| E | DNA (5'- D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3') | dna | 19 | — | — |
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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.75 | 0.92 | 27 | empty |
| 2 | 127 | 0.56 | 0.83 | 20 | empty |
| 3 | 143 | 0.43 | 0.76 | 15 | empty |
| 4 | 95 | 0.42 | 0.79 | 18 | empty |
| 5 | 58 | 0.30 | 0.76 | 9 | empty |
Interfaces
3 interfaces between chains.
- D–E · 852 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–D · 786 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–E · 728 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4F6M · Crystal structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding… · 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 4F6M · PDBe 4F6M · UniProt Q86T24
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