Research workbench
Notum complex with ARUK3003910
Analyse Notum complex with ARUK3003910 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B2Y
- Type
- protein
- Length
- 355 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
- SRQ, NAG, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 355 | 33% helix, 18% strand | Q6P988 |
Ligands and binding sites
- SRQ · 2,2-bis(fluoranyl)ethyl 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- GOL · Glycerol · 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 | 80 | 0.71 | 0.95 | 15 | SRQ |
| 2 | 170 | 0.48 | 0.76 | 21 | empty |
| 3 | 60 | 0.33 | 0.77 | 19 | SO4, EDO |
Modifications
Observed in the structure: 7 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 7B2Y · Notum complex with ARUK3003910 · 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 7B2Y · PDBe 7B2Y · UniProt Q6P988
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.