Research workbench
Structure of the wnt deacylase notum - crystal form I apo - 2.2A
Analyse Structure of the wnt deacylase notum - crystal form I apo - 2.2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WBH
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein notum homolog
- EC
- 3.-.-.-
- UniProt
- Q6P988
- Ligands
- NAG, CL, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein notum homolog (EC 3.-.-.-) | protein | 347 | 34% helix, 17% strand | Q6P988 |
| B | Protein notum homolog (EC 3.-.-.-) | protein | 351 | 33% helix, 17% strand | Q6P988 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.76 | 0.96 | 20 | empty |
| 2 | 137 | 0.69 | 0.89 | 33 | empty |
| 3 | 93 | 0.36 | 0.75 | 25 | empty |
| 4 | 54 | 0.33 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4WBH · Structure of the wnt deacylase notum - crystal form I apo - 2.2A · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6P988
- Elsewhere: RCSB PDB 4WBH · PDBe 4WBH · UniProt Q6P988
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