Research workbench
ZBTB7A zinc finger domain bound to DNA duplex containing ggaccc (oligo 20)
Analyse ZBTB7A zinc finger domain bound to DNA duplex containing ggaccc (oligo 20) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N5V
- Type
- protein + DNA
- Length
- 321 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger and btb domain-containing protein 7A; DNA strand I; DNA strand II
- UniProt
- O95365
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Zinc finger and btb domain-containing protein 7A | protein | 56 | 34% helix, 11% strand | O95365 |
| B | Zinc finger and btb domain-containing protein 7A | protein | 113 | 39% helix, 14% strand | O95365 |
| X, H, D | DNA strand I | dna | 16 | — | — |
| Y, I, E | DNA strand II | dna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.78 | 0.95 | 27 | empty |
| 2 | 102 | 0.76 | 0.97 | 18 | empty |
| 3 | 759 | 0.68 | 0.76 | 68 | empty |
| 4 | 61 | 0.61 | 0.91 | 20 | empty |
| 5 | 52 | 0.60 | 0.93 | 14 | empty |
Interfaces
22 interfaces between chains.
- X–Y · 699 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- D–E · 696 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- H–I · 695 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–D · 640 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–X · 483 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7N5V · ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 20) · the same entry in another collection · chain E against E, TM-score 1.00
- O95365 · AlphaFold monomer V2.0 prediction for zinc finger and btb domain- containing protein 7A… · a predicted model of the same protein · chain A against A, TM-score 0.77
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 O95365
- Elsewhere: RCSB PDB 7N5V · PDBe 7N5V · UniProt O95365
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