Research workbench

Crystal structure of frizzled 5 crd in complex with F2.I Fab

Analyse Crystal structure of frizzled 5 crd in complex with F2.I Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O39
Type: protein
Length: 550 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody F2.I Fab, light chain; Antibody F2.I Fab, heavy chain; Frizzled-5
UniProt: Q13467
Ligands: NAG
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody F2.I Fab, light chain	protein	212	6% helix, 52% strand	—
B	Antibody F2.I Fab, heavy chain	protein	218	8% helix, 52% strand	—
C	Frizzled-5	protein	120	43% helix, 6% strand	Q13467

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.63	0.74	65	EDO
2	193	0.46	0.74	31	empty
3	99	0.44	0.78	25	empty
4	153	0.41	0.73	25	EDO
5	88	0.39	0.77	18	empty

Interfaces

3 interfaces between chains.

A–B · 1853 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 804 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 225 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6O39 · Crystal structure of Frizzled 5 CRD in complex with F2.I Fab · the same entry in another collection · chain A against A, TM-score 1.00
Q13467 · AlphaFold monomer V2.0 prediction for frizzled-5 (Q13467) · 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 Q13467
Elsewhere: RCSB PDB 6O39 · PDBe 6O39 · UniProt Q13467

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.