MolNFT v1 · #137049 · protein + DNA

Zinc finger of human CXXC4 in complex with cpg DNA

5VC9: “Zinc finger of human CXXC4 in complex with cpg DNA”. X-ray diffraction, 2 ligands (ZN, UNX), 4 pockets (best druggability 0.64). MolNFT v1 #137049 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VC9
Type: protein + DNA
Length: 138 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cpg DNA; Cxxc-type zinc finger protein 4
UniProt: Q9H2H0
Ligands: ZN, UNX
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Cpg DNA	dna	12	—	—
C	Cxxc-type zinc finger protein 4	protein	46	33% helix, 0% strand	Q9H2H0
F	Cxxc-type zinc finger protein 4	protein	44	25% helix, 0% strand	Q9H2H0

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains C, F
UNX · Unknown atom or ion · ion · 7 copies · chains A, B, D, F, E

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

Pockets

4 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	445	0.64	0.78	38	UNX
2	326	0.55	0.75	26	empty
3	250	0.50	0.75	24	empty
4	198	0.48	0.76	23	empty

Interfaces

10 interfaces between chains.

A–B · 545 Å² buried · 51 hydrogen bonds · nucleic-nucleic
D–E · 542 Å² buried · 49 hydrogen bonds · nucleic-nucleic
A–C · 403 Å² buried · 10 hydrogen bonds · protein-nucleic
D–F · 382 Å² buried · 9 hydrogen bonds · protein-nucleic
B–C · 244 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

5VC9 · Zinc finger of human CXXC4 in complex with CpG DNA · the same entry in another collection · chain F against F, TM-score 1.00
Q9H2H0 · AlphaFold monomer V2.0 prediction for cxxc-type zinc finger protein 4 (Q9H2H0) · a predicted model of the same protein · chain F against A, TM-score 0.91

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 Q9H2H0
Elsewhere: RCSB PDB 5VC9 · PDBe 5VC9 · UniProt Q9H2H0

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