MolNFT v1 · #108186 · protein
Structure of the wnt deacylase notum - crystal form V - sos complex - 1.9A
4UZ6 · Protein notum homolog: “Structure of the wnt deacylase notum - crystal form V - sos complex - 1.9A”. X-ray diffraction, 4 ligands (GU4, YYJ, NAG), 6 pockets (best druggability 0.77). MolNFT v1 #108186 on GenesisL1: 3D structure…
- PDB
- 4UZ6
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein notum homolog
- EC
- 3.1.1.1
- UniProt
- Q6P988
- Ligands
- GU4, YYJ, NAG, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein notum homolog (EC 3.1.1.1) | protein | 351 | 34% helix, 17% strand | Q6P988 |
| B | Protein notum homolog (EC 3.1.1.1) | protein | 355 | 32% helix, 17% strand | Q6P988 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.77 | 0.99 | 19 | empty |
| 2 | 89 | 0.74 | 0.96 | 20 | empty |
| 3 | 508 | 0.72 | 0.81 | 41 | GU4, YYJ |
| 4 | 249 | 0.54 | 0.76 | 31 | empty |
| 5 | 166 | 0.50 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4UZ6 · Structure of the wnt deacylase notum - crystal form V - sos complex - 1.9A · 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 4UZ6 · PDBe 4UZ6 · UniProt Q6P988
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