MolNFT v1 · #105349 · protein + DNA

EGR1/ZIF268 zinc fingers in complex with methylated DNA

4R2A · Early growth response protein 1: “EGR1/ZIF268 zinc fingers in complex with methylated DNA”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.60). MolNFT v1 #105349 on GenesisL1: 3D structure, binding sites and…

PDB: 4R2A
Type: protein + DNA
Length: 108 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*(5CM)P*GP*T)-3'); DNA…
UniProt: P18146
Ligands: ZN
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Early growth response protein 1	protein	86	41% helix, 14% strand	P18146
B	DNA (5'-D(APGPCPGPTPGPGPGP(5CM)PGP*T)-3')	dna	11	—	—
C	DNA (5'-D(TPAP(5CM)PGPCPCPCPAPCPGP*C)-3')	dna	11	—	—

Ligands and binding sites

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

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	83	0.60	0.89	18	empty
2	54	0.56	0.90	15	empty
3	58	0.32	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 972 Å² buried · 22 hydrogen bonds · protein-nucleic
A–C · 552 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 479 Å² buried · 37 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

4R2A · Egr1/Zif268 zinc fingers in complex with methylated 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 0.95

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 4R2A · PDBe 4R2A · UniProt P18146

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