MolNFT v1 · #81215 · protein + DNA

Crystal structure of ZNF217 bound to DNA

3UK3 · 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP…: “Crystal structure of ZNF217 bound to DNA”. X-ray diffraction, 2 ligands (ZN, CL), 3 pockets (best druggability 0.58). MolNFT v1 #81215 on GenesisL1: 3D structure…

PDB: 3UK3
Type: protein + DNA
Length: 146 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP *CP*A)-3'…
UniProt: O75362
Ligands: ZN, CL
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(TPTPTPGPCPAPGPAPAPTPCPGPAPTPTPCPTPGP CPA)-3'	dna	20	—	—
B	5'-D(APAPTPGPCPAPGPAPAPTPCPGPAPTPTPCPTPGP CPA)-3'	dna	20	—	—
C	Zinc finger protein 217	protein	52	44% helix, 12% strand	O75362
D	Zinc finger protein 217	protein	54	43% helix, 11% strand	O75362

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, D, C
CL · Chloride ion · ion · chains C

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	67	0.58	0.89	19	empty
2	70	0.57	0.88	20	empty
3	259	0.48	0.74	28	empty

Interfaces

5 interfaces between chains.

A–B · 865 Å² buried · 76 hydrogen bonds · nucleic-nucleic
A–C · 584 Å² buried · 9 hydrogen bonds · protein-nucleic
B–D · 543 Å² buried · 9 hydrogen bonds · protein-nucleic
B–C · 358 Å² buried · 4 hydrogen bonds · protein-nucleic
A–D · 337 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

3UK3 · Crystal structure of ZNF217 bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
O75362 · AlphaFold monomer V2.0 prediction for zinc finger protein 217 (O75362) · a predicted model of the same protein · chain C against A, TM-score 0.80

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 O75362
Elsewhere: RCSB PDB 3UK3 · PDBe 3UK3 · UniProt O75362

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