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Structural basis of selective binding of nonmethylated cpg islands by the cxxc domain of CFP1

Analyse Structural basis of selective binding of nonmethylated cpg islands by the cxxc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QMB
Type: protein + DNA
Length: 78 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cpg-binding protein; 5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3'
UniProt: Q9P0U4
Ligands: ZN, CA
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cpg-binding protein	protein	54	26% helix, 4% strand	Q9P0U4
B, C	5'-D(GPCPCPAPCPCPGPGPTPGPGPC)-3'	dna	12	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
CA · Calcium ion · metal · chains B, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.25	0.72	11	empty

Interfaces

3 interfaces between chains.

B–C · 565 Å² buried · 61 hydrogen bonds · nucleic-nucleic
A–C · 418 Å² buried · 11 hydrogen bonds · protein-nucleic
A–B · 302 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

3QMB · Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of… · the same entry in another collection · chain A against A, TM-score 1.00
Q9P0U4 · AlphaFold monomer V2.0 prediction for cxxc-type zinc finger protein 1 (Q9P0U4) · 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 Q9P0U4
Elsewhere: RCSB PDB 3QMB · PDBe 3QMB · UniProt Q9P0U4

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