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MOUSEZFP568-ZNF1-10 in complex with DNA

Analyse MOUSEZFP568-ZNF1-10 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5V3J
Type: protein + DNA
Length: 659 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (26-mer); Zinc finger protein 568
UniProt: E9PYI1
Ligands: ZN, MG
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA (26-mer)	dna	26	—	—
B, D	DNA (26-mer)	dna	26	—	—
E	Zinc finger protein 568	protein	277	41% helix, 13% strand	E9PYI1
F	Zinc finger protein 568	protein	278	41% helix, 14% strand	E9PYI1

Ligands and binding sites

ZN · Zinc ion · metal · 20 copies · chains E, F
MG · Magnesium ion · metal · 2 copies · chains E, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains E, F

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	892	0.78	0.81	65	empty
2	980	0.75	0.78	74	empty
3	368	0.72	0.84	36	empty
4	558	0.72	0.81	58	empty
5	162	0.64	0.86	28	empty

Interfaces

7 interfaces between chains.

A–E · 2019 Å² buried · 52 hydrogen bonds · protein-nucleic
C–F · 1952 Å² buried · 53 hydrogen bonds · protein-nucleic
D–F · 1277 Å² buried · 17 hydrogen bonds · protein-nucleic
B–E · 1274 Å² buried · 19 hydrogen bonds · protein-nucleic
A–B · 1199 Å² buried · 106 hydrogen bonds · nucleic-nucleic

Compared structures

5V3J · mouseZFP568-ZnF1-10 in complex with DNA · the same entry in another collection · chain F against F, TM-score 1.00
E9PYI1 · AlphaFold monomer V2.0 prediction for zinc finger protein 568 (E9PYI1) · a predicted model of the same protein · chain F against A, TM-score 0.60

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 E9PYI1
Elsewhere: RCSB PDB 5V3J · PDBe 5V3J · UniProt E9PYI1

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