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ZBTB7A zinc finger domain bound to DNA duplex containing ggaccc (oligo 23)

Analyse ZBTB7A zinc finger domain bound to DNA duplex containing ggaccc (oligo 23) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N5W
Type: protein + DNA
Length: 117 residues
Chains: 3
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: 3 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Zinc finger and btb domain-containing protein 7A	protein	85	33% helix, 16% strand	O95365
X	DNA strand I	dna	16	—	—
Y	DNA strand II	dna	16	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A, X, Y

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.62	0.89	13	empty
2	173	0.50	0.78	32	empty
3	54	0.30	0.76	16	empty

Interfaces

3 interfaces between chains.

X–Y · 664 Å² buried · 63 hydrogen bonds · nucleic-nucleic
A–X · 503 Å² buried · 15 hydrogen bonds · protein-nucleic
A–Y · 349 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

7N5W · ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 23) · the same entry in another collection · chain A against A, 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 0.56

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 7N5W · PDBe 7N5W · UniProt O95365

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