MolNFT v1 · #124402 · protein + DNA

Mouse KLF4 ZNF1-3 and TPG/MPA sequence DNA complex structure

5KE7 · Krueppel-like factor 4: “Mouse KLF4 ZNF1-3 and TPG/MPA sequence DNA complex structure”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.64). MolNFT v1 #124402 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5KE7
Type: protein + DNA
Length: 107 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Krueppel-like factor 4; DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3'); DNA…
UniProt: Q60793
Ligands: ZN
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Krueppel-like factor 4	protein	87	38% helix, 14% strand	Q60793
B	DNA (5'-D(GPAPGPGPTPGPTPGPGPC)-3')	dna	10	—	—
C	DNA (5'-D(GPCPCPAP(5CM)PAPCPCPTPC)-3')	dna	10	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B

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	168	0.64	0.86	28	EDO
2	61	0.60	0.92	13	EDO
3	99	0.49	0.82	21	empty
4	55	0.27	0.74	15	empty

Interfaces

3 interfaces between chains.

A–B · 656 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 445 Å² buried · 37 hydrogen bonds · nucleic-nucleic
A–C · 422 Å² buried · 5 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5KE7 · mouse Klf4 ZnF1-3 and TpG/MpA sequence DNA complex structure · 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 0.91

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 Q60793
Elsewhere: RCSB PDB 5KE7 · PDBe 5KE7 · UniProt Q60793

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