MolNFT v1 · #108204 · protein
Structure of the wnt deacylase notum in complex with O-palmitoleoyl serine - crystal form IX - 1.5A
4UZQ · Protein notum homolog: “Structure of the wnt deacylase notum in complex with O-palmitoleoyl serine - crystal form IX - 1.5A”. X-ray diffraction, 4 ligands (PAM, NAG, NA), 2 pockets (best druggability 0.80). MolNFT v1 #108204 on…
- PDB
- 4UZQ
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein notum homolog; Protein wnt-7A
- EC
- 3.1.1.1
- UniProt
- Q6P988, O00755
- Ligands
- PAM, NAG, NA, CL
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein notum homolog (EC 3.1.1.1) | protein | 355 | 32% helix, 17% strand | Q6P988 |
| B | Protein wnt-7A | protein | 1 | 0% helix, 0% strand | O00755 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.80 | 0.99 | 19 | PAM |
| 2 | 53 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 132 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 4UZQ · Structure of the wnt deacylase notum in complex with O-palmitoleoyl serine - crystal form… · 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
- Every structure of UniProt O00755
- Elsewhere: RCSB PDB 4UZQ · PDBe 4UZQ · UniProt Q6P988 · UniProt O00755
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