MolNFT v1 · #52808 · protein + DNA

Crystal structure of the zinc finger domain of KLF4 bound to its target DNA

2WBS · Krueppel-like factor 4: “Crystal structure of the zinc finger domain of KLF4 bound to its target DNA”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.27). MolNFT v1 #52808 on GenesisL1: 3D structure, binding sites…

PDB: 2WBS
Type: protein + DNA
Length: 101 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Krueppel-like factor 4; 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'; 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'
UniProt: Q60793
Ligands: ZN
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Krueppel-like factor 4	protein	87	36% helix, 14% strand	Q60793
F	5'-D(GPAPGPGPCPGP*CP)-3'	dna	7	—	—
G	5'-D(GPCPGPCPCPTP*CP)-3'	dna	7	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A
GOL · Glycerol · additive · chains A

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	51	0.27	0.75	13	empty

Interfaces

3 interfaces between chains.

A–F · 489 Å² buried · 11 hydrogen bonds · protein-nucleic
F–G · 326 Å² buried · 28 hydrogen bonds · nucleic-nucleic
A–G · 254 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

2WBS · Crystal structure of the zinc finger domain of Klf4 bound to its target DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q60793 · AlphaFold monomer V2.0 prediction for krueppel-like factor 4 (Q60793) · a predicted model of the same protein · chain A against A, TM-score 0.66

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 Q60793
Elsewhere: RCSB PDB 2WBS · PDBe 2WBS · UniProt Q60793

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