Research workbench
Crystal structure of the cysteine-rich domain of human frizzled 4 - crystal form II
Analyse Crystal structure of the cysteine-rich domain of human frizzled 4 - crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BPQ
- Type
- protein
- Length
- 475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Frizzled-4
- UniProt
- Q9ULV1
- Ligands
- NAG, CL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Frizzled-4 | protein | 119 | 41% helix, 12% strand | Q9ULV1 |
| C | Frizzled-4 | protein | 118 | 42% helix, 7% strand | Q9ULV1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.57 | 0.83 | 28 | empty |
| 2 | 221 | 0.47 | 0.74 | 31 | empty |
| 3 | 55 | 0.39 | 0.80 | 12 | empty |
| 4 | 81 | 0.39 | 0.77 | 14 | empty |
| 5 | 61 | 0.29 | 0.73 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–D · 715 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 296 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5BPQ · Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form II · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ULV1 · AlphaFold monomer V2.0 prediction for frizzled-4 (Q9ULV1) · a predicted model of the same protein · chain A 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 Q9ULV1
- Elsewhere: RCSB PDB 5BPQ · PDBe 5BPQ · UniProt Q9ULV1
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