Research workbench
Notum FRAGMENT_3 (4H,5H-NAPHTHO[1,2-B]THIOPHENE-2-carboxylic acid)
Analyse Notum FRAGMENT_3 (4H,5H-NAPHTHO[1,2-B]THIOPHENE-2-carboxylic acid) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BN8
- Type
- protein
- Length
- 348 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
- U4T, NAG, SO4
- Pockets
- 2 · best druggability 0.74
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 | 348 | 33% helix, 18% strand | Q6P988 |
Ligands and binding sites
- U4T · 4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 4 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 | 0.74 | 0.94 | 18 | U4T |
| 2 | 52 | 0.30 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BN8 · Notum fragment_3 (4H,5H-naphtho[1,2-b]thiophene-2-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 7BN8 · PDBe 7BN8 · UniProt Q6P988
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