Research workbench

ZNF410 zinc fingers 1-5 with 17 mer blunt DNA oligonucleotide

Analyse ZNF410 zinc fingers 1-5 with 17 mer blunt DNA oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WMI
Type: protein + DNA
Length: 360 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zinc finger protein 410; DNA (5'- D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3'…
UniProt: Q86VK4
Ligands: ZN
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Zinc finger protein 410	protein	146	40% helix, 12% strand	Q86VK4
B, E	DNA (5'- D(CPAPCPAPTPCPCPCPAPTPAPAPTPAPAPTP*G)-3')	dna	17	—	—
C, F	DNA (5'- D(CPAPTPTPAPTPTPAPTPGPGPGPAPTPGPTP*G)-3')	dna	17	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, D
EDO · 1,2-ethanediol · additive · 2 copies · chains A, E, D, C

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	592	0.71	0.80	63	EDO
2	535	0.70	0.79	63	EDO
3	59	0.45	0.83	14	empty
4	70	0.43	0.81	13	empty

Interfaces

8 interfaces between chains.

A–E · 1443 Å² buried · 19 hydrogen bonds · protein-nucleic
D–B · 1429 Å² buried · 18 hydrogen bonds · protein-nucleic
B–C · 775 Å² buried · 66 hydrogen bonds · nucleic-nucleic
E–F · 769 Å² buried · 61 hydrogen bonds · nucleic-nucleic
A–F · 682 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6WMI · ZNF410 zinc fingers 1-5 with 17 mer blunt DNA Oligonucleotide · the same entry in another collection · chain B against B, TM-score 1.00
Q86VK4 · AlphaFold monomer V2.0 prediction for zinc finger protein 410 (Q86VK4) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q86VK4
Elsewhere: RCSB PDB 6WMI · PDBe 6WMI · UniProt Q86VK4

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