Research workbench
Kaiso (ZBTB33) E535Q mutant zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs)
Analyse Kaiso (ZBTB33) E535Q mutant zinc finger DNA binding domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VMZ
- Type
- protein + DNA
- Length
- 158 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*(5CM)P*GP*(5CM)…
- UniProt
- Q86T24
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator kaiso | protein | 122 | 33% helix, 21% strand | Q86T24 |
| D | DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*(5CM)P*GP*(5CM) P*GP*AP*AP*TP*AP*AP*CP*G)-3') | dna | 18 | — | — |
| E | DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*(5CM)P*GP*(5CM) P*GP*GP*GP*AP*AP*GP*CP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- TLA · L(+)-tartaric acid · additive · chains A, D, E
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 | 158 | 0.72 | 0.90 | 22 | TLA |
| 2 | 130 | 0.53 | 0.81 | 20 | empty |
| 3 | 104 | 0.41 | 0.77 | 14 | empty |
| 4 | 112 | 0.39 | 0.76 | 19 | empty |
| 5 | 97 | 0.33 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–E · 853 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–E · 838 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–D · 825 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5VMZ · Kaiso (ZBTB33) E535Q mutant zinc finger DNA binding domain in complex with a double… · 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 5VMZ · PDBe 5VMZ · UniProt Q86T24
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