Research workbench

Designed repeat protein in complex with FZ7

Analyse Designed repeat protein in complex with FZ7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NE2
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Designed repeat protein binder; Frizzled-7
UniProt: O75084
Ligands: NAG, SO4
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Designed repeat protein binder	protein	193	55% helix, 0% strand	—
A	Frizzled-7	protein	119	39% helix, 9% strand	O75084

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 10 copies · chains B, A
ACT · Acetate ion · additive · 9 copies · chains B, A
EDO · 1,2-ethanediol · additive · 2 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	108	0.37	0.75	18	ACT
2	61	0.32	0.76	15	SO4

Interfaces

1 interface between chains.

B–A · 1162 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6NE2 · Designed repeat protein in complex with Fz7 · the same entry in another collection · chain B against B, TM-score 1.00
O75084 · AlphaFold monomer V2.0 prediction for frizzled-7 (O75084) · a predicted model of the same protein · chain A 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 O75084
Elsewhere: RCSB PDB 6NE2 · PDBe 6NE2 · UniProt O75084

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