MolNFT v1 · #156993 · protein + DNA
ZBTB24 zinc fingers 4-8 with 19+1MER DNA oligonucleotide (sequence 4 with a cpg 5MC modification)
6ML7 · Zinc finger and btb domain-containing protein 24: “ZBTB24 zinc fingers 4-8 with 19+1MER DNA oligonucleotide (sequence 4 with a cpg 5MC modification)”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 6ML7
- Type
- protein + DNA
- Length
- 183 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…
- UniProt
- Q80X44
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger and btb domain-containing protein 24 | protein | 143 | 43% helix, 13% strand | Q80X44 |
| E | DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*(5CM) P*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 · 3 copies · chains A, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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 | 408 | 0.61 | 0.76 | 29 | empty |
| 2 | 165 | 0.60 | 0.83 | 17 | empty |
| 3 | 117 | 0.58 | 0.85 | 22 | empty |
| 4 | 57 | 0.50 | 0.87 | 18 | empty |
| 5 | 113 | 0.41 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1187 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–F · 897 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–F · 753 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6ML7 · ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpG 5mC… · 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 6ML7 · PDBe 6ML7 · UniProt Q80X44
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