MolNFT v1 · #174187 · protein
Notum ARUK3003710
7BNL · Palmitoleoyl-protein carboxylesterase notum: “Notum ARUK3003710”. X-ray diffraction, 3 ligands (U5T, NAG, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #174187 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BNL
- Type
- protein
- Length
- 350 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
- U5T, NAG, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 350 | 34% helix, 18% strand | Q6P988 |
Ligands and binding sites
- U5T · (4~{E})-2-(3,4-dimethylphenyl)-4-[(1-methylpyrazol-4-yl)methylidene]-1,3-oxazol-5-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 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 | 105 | 0.72 | 0.93 | 19 | U5T |
| 2 | 84 | 0.41 | 0.79 | 25 | SO4 |
| 3 | 62 | 0.27 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BNL · Notum ARUK3003710 · 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 7BNL · PDBe 7BNL · UniProt Q6P988
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