MolNFT v1 · #124642 · protein + DNA

Wilms tumor protein (WT1) ZNF2-4 Q369H in complex with DNA

5KL3: “Wilms tumor protein (WT1) ZNF2-4 Q369H in complex with DNA”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.64). MolNFT v1 #124642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KL3
Type: protein + DNA
Length: 109 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wilms tumor protein; DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3'); DNA…
UniProt: P19544
Ligands: ZN
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Wilms tumor protein	protein	87	39% helix, 14% strand	P19544
B	DNA (5'-D(APGPCPGPTPGPGPGPAPGP*T)-3')	dna	11	—	—
C	DNA (5'-D(TPAPCPTPCPCPCPAPCPGP*C)-3')	dna	11	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A
EDO · 1,2-ethanediol · additive · chains A, B, 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	60	0.64	0.94	16	EDO
2	65	0.61	0.91	17	empty
3	54	0.28	0.75	12	empty

Interfaces

3 interfaces between chains.

A–B · 971 Å² buried · 20 hydrogen bonds · protein-nucleic
A–C · 553 Å² buried · 6 hydrogen bonds · protein-nucleic
B–C · 472 Å² buried · 35 hydrogen bonds · nucleic-nucleic

Compared structures

5KL3 · Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
P19544 · AlphaFold monomer V2.0 prediction for wilms tumor protein (P19544) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P19544
Elsewhere: RCSB PDB 5KL3 · PDBe 5KL3 · UniProt P19544

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