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Frizzled-8 complex with designed surrogate wnt agonist, A1 dataset

Analyse Frizzled-8 complex with designed surrogate wnt agonist, A1 dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UN6
Type: protein
Length: 826 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Frizzled-8; Designed wnt agonist B12
UniProt: Q9H461
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 70% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Frizzled-8	protein	119	44% helix, 8% strand	Q9H461
E	Designed wnt agonist B12	protein	89	89% helix, 0% strand	—
F	Designed wnt agonist B12	protein	88	89% helix, 0% strand	—
G	Designed wnt agonist B12	protein	87	89% helix, 0% strand	—
H	Designed wnt agonist B12	protein	84	88% helix, 0% strand	—
B, D	Frizzled-8	protein	120	43% helix, 6% strand	Q9H461

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.78	0.80	79	empty
2	1177	0.72	0.75	105	empty
3	326	0.54	0.74	44	empty
4	213	0.51	0.76	25	empty
5	90	0.38	0.76	18	empty

Interfaces

11 interfaces between chains.

A–E · 786 Å² buried · 4 hydrogen bonds · protein-protein
G–C · 758 Å² buried · 2 hydrogen bonds · protein-protein
F–B · 744 Å² buried · 4 hydrogen bonds · protein-protein
H–D · 742 Å² buried · 1 hydrogen bond · protein-protein
E–B · 519 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

5UN6 · Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset · the same entry in another collection · chain D against D, TM-score 1.00
Q9H461 · AlphaFold monomer V2.0 prediction for frizzled-8 (Q9H461) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q9H461
Elsewhere: RCSB PDB 5UN6 · PDBe 5UN6 · UniProt Q9H461

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