MolNFT v1 · #136407 · protein
Crystal structure of frizzled 5 crd in complex with bog
5URZ · Frizzled-5: “Crystal structure of frizzled 5 crd in complex with bog”. X-ray diffraction, 2 ligands (FUC, NAG), 5 pockets (best druggability 0.41). MolNFT v1 #136407 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5URZ
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Frizzled-5
- UniProt
- Q13467
- Ligands
- FUC, NAG
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Frizzled-5 | protein | 119 | 43% helix, 8% strand | Q13467 |
| B | Frizzled-5 | protein | 119 | 44% helix, 7% strand | Q13467 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- BOG · octyl beta-D-glucopyranoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.41 | 0.77 | 24 | empty |
| 2 | 78 | 0.37 | 0.77 | 12 | empty |
| 3 | 71 | 0.35 | 0.76 | 12 | empty |
| 4 | 72 | 0.35 | 0.76 | 18 | empty |
| 5 | 52 | 0.31 | 0.76 | 12 | BOG |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 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 Q13467
- Elsewhere: RCSB PDB 5URZ · PDBe 5URZ · UniProt Q13467
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