Research workbench
Crystal structure of the cysteine-rich domain of human frizzled 4 - crystal form I
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
- 5BPB
- Type
- protein
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Frizzled-4
- UniProt
- Q9ULV1
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Frizzled-4 | protein | 119 | 44% helix, 12% strand | Q9ULV1 |
| B | Frizzled-4 | protein | 127 | 41% helix, 11% strand | Q9ULV1 |
| D | Frizzled-4 | protein | 130 | 38% helix, 7% strand | Q9ULV1 |
| C | Frizzled-4 | protein | 118 | 42% helix, 8% strand | Q9ULV1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.87 | 0.88 | 96 | empty |
| 2 | 155 | 0.59 | 0.83 | 29 | empty |
| 3 | 69 | 0.37 | 0.78 | 19 | empty |
| 4 | 60 | 0.32 | 0.76 | 17 | empty |
| 5 | 62 | 0.31 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 688 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 400 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 380 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5BPB · Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form I · the same entry in another collection · chain C against C, TM-score 1.00
- Q9ULV1 · AlphaFold monomer V2.0 prediction for frizzled-4 (Q9ULV1) · 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 Q9ULV1
- Elsewhere: RCSB PDB 5BPB · PDBe 5BPB · UniProt Q9ULV1
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