Research workbench

EGR1/ZIF268 zinc fingers in complex with formylated DNA

Analyse EGR1/ZIF268 zinc fingers in complex with formylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R2D
Type: protein + DNA
Length: 109 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Early growth response protein 1; DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3'); DNA…
UniProt: P18146
Ligands: ZN
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Early growth response protein 1	protein	87	40% helix, 14% strand	P18146
B	DNA (5'-D(APGPCPGPTPGPGPGP(5FC)PGP*T)-3')	dna	11	—	—
C	DNA (5'-D(TPAP(5FC)PGPCPCPCPAPCPGP*C)-3')	dna	11	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.61	0.90	16	empty

Interfaces

3 interfaces between chains.

A–B · 966 Å² buried · 22 hydrogen bonds · protein-nucleic
A–C · 576 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 480 Å² buried · 49 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4R2D · Egr1/Zif268 zinc fingers in complex with formylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
P18146 · AlphaFold monomer V2.0 prediction for early growth response protein 1 (P18146) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P18146
Elsewhere: RCSB PDB 4R2D · PDBe 4R2D · UniProt P18146

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