Research workbench
Crystal structure of norrin, a wnt signalling activator, crystal form II
Analyse Crystal structure of norrin, a wnt signalling activator, crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BQ8
- Type
- protein
- Length
- 402 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 0.58
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Norrin | protein | 104 | 0% helix, 63% strand | Q00604 |
| B | Norrin | protein | 97 | 0% helix, 69% strand | Q00604 |
| C | Norrin | protein | 99 | 0% helix, 67% strand | Q00604 |
| D | Norrin | protein | 102 | 0% helix, 71% strand | Q00604 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
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 | 52 | 0.58 | 0.91 | 19 | empty |
| 2 | 51 | 0.29 | 0.75 | 13 | empty |
| 3 | 52 | 0.29 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1990 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1904 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 501 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 11 modified (disulfide, methylation).
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 Q00604
- Elsewhere: RCSB PDB 5BQ8 · PDBe 5BQ8 · UniProt Q00604
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