MolNFT v1 · #114467 · protein
Crystal structure of norrin, a wnt signalling activator, crystal form III
5BQB: “Crystal structure of norrin, a wnt signalling activator, crystal form III”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.56). MolNFT v1 #114467 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BQB
- Type
- protein
- Length
- 393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Norrin
- UniProt
- Q00604
- Ligands
- CL
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Norrin | protein | 99 | 0% helix, 65% strand | Q00604 |
| B, C, D | Norrin | protein | 98 | 0% helix, 65% strand | Q00604 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.56 | 0.89 | 19 | empty |
| 2 | 87 | 0.35 | 0.75 | 16 | empty |
| 3 | 54 | 0.32 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1766 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1688 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- Q00604 · AlphaFold monomer V2.0 prediction for norrin (Q00604) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q00604
- Elsewhere: RCSB PDB 5BQB · PDBe 5BQB · UniProt Q00604
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