Research workbench
Structure of the wnt deacylase notum in complex with a pyrrolidine-3- carboxylic acid fragment 587
Analyse Structure of the wnt deacylase notum in complex with a pyrrolidine-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YV0
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoleoyl-protein carboxylesterase notum
- EC
- 3.1.1.98
- UniProt
- Q6P988
- Ligands
- PQT, NAG, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 359 | 32% helix, 17% strand | Q6P988 |
Ligands and binding sites
- PQT · (3~{R})-1-(2-chlorophenyl)pyrrolidine-3-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.73 | 0.93 | 19 | PQT |
| 2 | 53 | 0.31 | 0.77 | 15 | EDO |
| 3 | 52 | 0.30 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6YV0 · Structure of the wnt deacylase notum in complex with a pyrrolidine-3-carboxylic acid… · 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 6YV0 · PDBe 6YV0 · UniProt Q6P988
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