Research workbench
Crystal structure of Frizzled 7 CRD in complex with F7.B Fab
Analyse Crystal structure of Frizzled 7 CRD in complex with F7.B Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O3A
- Type
- protein
- Length
- 548 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens
- Molecule
- Antibody F7.B Fab, Light chain; Antibody F7.B Fab, Heavy chain; Frizzled-7
- UniProt
- O75084
- Ligands
- NAG, NA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody F7.B Fab, Light chain | protein | 212 | 6% helix, 52% strand | — |
| B | Antibody F7.B Fab, Heavy chain | protein | 218 | 8% helix, 54% strand | — |
| E | Frizzled-7 | protein | 118 | 44% helix, 8% strand | O75084 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.64 | 0.83 | 29 | CXS |
| 2 | 515 | 0.59 | 0.74 | 58 | EDO |
| 3 | 123 | 0.56 | 0.83 | 20 | empty |
| 4 | 74 | 0.39 | 0.78 | 14 | empty |
| 5 | 74 | 0.29 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1844 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 632 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 265 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 6O3A · PDBe 6O3A · UniProt O75084
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.