MolNFT v1 · #146389 · protein + DNA

Remodeled crystal structure of DNA-bound DUX4-HD2

6DFY · Double homeobox protein 4: “Remodeled crystal structure of DNA-bound DUX4-HD2”. X-ray diffraction, 2 pockets (best druggability 0.44). MolNFT v1 #146389 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DFY
Type: protein + DNA
Length: 133 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Double homeobox protein 4; DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'); DNA…
UniProt: Q9UBX2
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Double homeobox protein 4	protein	54	67% helix, 0% strand	Q9UBX2
E	DNA (5'-D(APAPGPAPTPTPAPGPAPTPTPAPGPT)-3')	dna	14	—	—
F	DNA (5'-D(TPTPCPTPAPAPTPCPTPAPAPTPCPA)-3')	dna	13	—	—
D	Double homeobox protein 4	protein	52	69% helix, 0% strand	Q9UBX2

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.44	0.75	20	empty
2	141	0.43	0.76	24	empty

Interfaces

5 interfaces between chains.

E–F · 488 Å² buried · 32 hydrogen bonds · nucleic-nucleic
E–D · 351 Å² buried · 9 hydrogen bonds · protein-nucleic
C–E · 325 Å² buried · 6 hydrogen bonds · protein-nucleic
C–F · 288 Å² buried · 4 hydrogen bonds · protein-nucleic
F–D · 265 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6DFY · Remodeled crystal structure of DNA-bound DUX4-HD2 · the same entry in another collection · chain C against C, TM-score 1.00
Q9UBX2 · AlphaFold monomer V2.0 prediction for double homeobox protein 4 (Q9UBX2) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 Q9UBX2
Elsewhere: RCSB PDB 6DFY · PDBe 6DFY · UniProt Q9UBX2

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