Research workbench

Zinc finger of human CXXC5 in complex with cpg DNA

Analyse Zinc finger of human CXXC5 in complex with cpg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W9S
Type: protein + DNA
Length: 68 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cpg DNA fragment; Cxxc-type zinc finger protein 5
UniProt: Q7LFL8
Ligands: ZN, SO4, UNX
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cpg DNA fragment	dna	12	—	—
C	Cxxc-type zinc finger protein 5	protein	44	34% helix, 0% strand	Q7LFL8

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains C
SO4 · Sulfate ion · ion · chains C
UNX · Unknown atom or ion · ion · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.51	0.77	23	empty
2	123	0.44	0.78	17	UNX

Interfaces

3 interfaces between chains.

A–B · 544 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–C · 414 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 353 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

5W9S · Zinc finger of human CXXC5 in complex with CpG DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q7LFL8 · AlphaFold monomer V2.0 prediction for cxxc-type zinc finger protein 5 (Q7LFL8) · a predicted model of the same protein · chain C 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 Q7LFL8
Elsewhere: RCSB PDB 5W9S · PDBe 5W9S · UniProt Q7LFL8

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