MolNFT v1 · #171151 · protein
Structure of the wnt deacylase notum in complex with a pyrrole-3- carboxylic acid fragment 686
6YV4 · Palmitoleoyl-protein carboxylesterase notum: “Structure of the wnt deacylase notum in complex with a pyrrole-3- carboxylic acid fragment 686”. X-ray diffraction, 3 ligands (PQK, NAG, SO4), 2 pockets (best druggability 0.67). MolNFT…
- PDB
- 6YV4
- 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
- PQK, NAG, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 359 | 33% helix, 17% strand | Q6P988 |
Ligands and binding sites
- PQK · 1-cyclopropyl-2,5-dimethyl-pyrrole-3-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 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 | 105 | 0.67 | 0.90 | 25 | PQK |
| 2 | 98 | 0.39 | 0.77 | 26 | empty |
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6YV4 · Structure of the wnt deacylase notum in complex with a pyrrole-3-carboxylic acid fragment… · 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 6YV4 · PDBe 6YV4 · UniProt Q6P988
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