Research workbench
ZBTB24 zinc fingers 4-8 with 19+1MER DNA oligonucleotide (sequence 4)
Analyse ZBTB24 zinc fingers 4-8 with 19+1MER DNA oligonucleotide (sequence 4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ML5
- Type
- protein + DNA
- Length
- 182 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger and btb domain-containing protein 24; DNA (5'…
- UniProt
- Q80X44
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger and btb domain-containing protein 24 | protein | 142 | 42% helix, 13% strand | Q80X44 |
| E | DNA (5'- D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*TP*T)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*TP*AP*AP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.62 | 0.84 | 26 | empty |
| 2 | 415 | 0.62 | 0.77 | 24 | empty |
| 3 | 103 | 0.57 | 0.86 | 23 | empty |
| 4 | 50 | 0.50 | 0.88 | 17 | empty |
| 5 | 95 | 0.38 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1172 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–F · 903 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–F · 780 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6ML5 · ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4) · the same entry in another collection · chain A against A, TM-score 1.00
- Q80X44 · AlphaFold monomer V2.0 prediction for zinc finger and btb domain- containing protein 24… · a predicted model of the same protein · chain A against A, TM-score 0.69
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 Q80X44
- Elsewhere: RCSB PDB 6ML5 · PDBe 6ML5 · UniProt Q80X44
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