Research workbench

Mouse ZFP57 zinc fingers in complex with methylated DNA

Analyse Mouse ZFP57 zinc fingers in complex with methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GZN
Type: protein + DNA
Length: 81 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3'); DNA…
UniProt: Q8C6P8
Ligands: ZN, CA
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(TPAPTPTPGPCP(5CM)PGPCPAP*G)-3')	dna	11	—	—
B	DNA (5'-D(APCPTPGP(5CM)PGPGPCPAPAP*T)-3')	dna	11	—	—
C	Zinc finger protein 57	protein	59	39% helix, 14% strand	Q8C6P8

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains C
CA · Calcium ion · metal · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C
ACT · Acetate ion · additive · chains C

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	70	0.59	0.90	20	empty

Interfaces

3 interfaces between chains.

B–C · 657 Å² buried · 18 hydrogen bonds · protein-nucleic
A–C · 500 Å² buried · 12 hydrogen bonds · protein-nucleic
A–B · 461 Å² buried · 30 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

4GZN · Mouse ZFP57 zinc fingers in complex with methylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q8C6P8 · AlphaFold monomer V2.0 prediction for zinc finger protein 57 (Q8C6P8) · a predicted model of the same protein · chain C against A, TM-score 0.78

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 Q8C6P8
Elsewhere: RCSB PDB 4GZN · PDBe 4GZN · UniProt Q8C6P8

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