MolNFT v1 · #91218 · protein + DNA
Crystal structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA
4F6M · Transcriptional regulator kaiso: “Crystal structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.75). MolNFT v1 #91218 on…
- 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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