MolNFT v1 · #91219 · protein + DNA
Crystal structure of kaiso zinc finger DNA binding protein in complex with methylated cpg site DNA
4F6N · Transcriptional regulator kaiso: “Crystal structure of kaiso zinc finger DNA binding protein in complex with methylated cpg site DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.73). MolNFT v1 #91219 on…
- PDB
- 4F6N
- Type
- protein + DNA
- Length
- 157 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*TP*CP*AP*CP*(5CM)P*GP*(5CM)…
- UniProt
- Q86T24
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.73
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(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3') | dna | 19 | — | — |
| E | DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM) P*GP*GP*TP*GP*AP*CP*AP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
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 | 309 | 0.73 | 0.86 | 28 | GOL |
| 2 | 167 | 0.54 | 0.80 | 23 | empty |
| 3 | 153 | 0.43 | 0.76 | 17 | GOL |
| 4 | 77 | 0.32 | 0.75 | 17 | empty |
| 5 | 70 | 0.29 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- D–E · 854 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–E · 786 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 725 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4F6N · Crystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG… · 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 0.97
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 4F6N · PDBe 4F6N · UniProt Q86T24
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.