MolNFT v1 · #108179 · protein
Structure of the wnt deacylase notum - crystal form I heparin fragment complex - 1.7A
4UYW · Protein notum homolog: “Structure of the wnt deacylase notum - crystal form I heparin fragment complex - 1.7A”. X-ray diffraction, 3 ligands (UAP, NAG, SGN), 3 pockets (best druggability 0.76). MolNFT v1 #108179 on GenesisL1: 3D…
- PDB
- 4UYW
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein notum homolog
- UniProt
- Q6P988
- Ligands
- UAP, NAG, SGN
- Pockets
- 3 · 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 | protein | 346 | 35% helix, 17% strand | Q6P988 |
| B | Protein notum homolog | protein | 346 | 34% helix, 17% strand | Q6P988 |
Ligands and binding sites
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.76 | 0.97 | 18 | empty |
| 2 | 90 | 0.75 | 0.96 | 20 | empty |
| 3 | 69 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4UYW · Structure of the wnt deacylase notum - crystal form I heparin fragment complex - 1.7A · 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 4UYW · PDBe 4UYW · UniProt Q6P988
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