MolNFT v1 · #78926 · protein
Structures of Fab-protease complexes reveal a highly specific non- canonical mechanism of inhibition.
3SO3 · Suppressor of tumorigenicity 14 protein: “Structures of Fab-protease complexes reveal a highly specific non- canonical mechanism of inhibition.”. X-ray diffraction, 2 ligands (GLC, FRU), 5 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 3SO3
- Type
- protein
- Length
- 676 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of tumorigenicity 14 protein; A11 Fab light chain; A11 Fab heavy chain
- EC
- 3.4.21.109
- UniProt
- Q9Y5Y6
- Ligands
- GLC, FRU
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 240 | 10% helix, 36% strand | Q9Y5Y6 |
| B | A11 Fab light chain | protein | 216 | 7% helix, 56% strand | — |
| C | A11 Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains B, C
- FRU · beta-D-fructofuranose · sugar · chains B, C
- GOL · Glycerol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.74 | 0.86 | 44 | empty |
| 2 | 291 | 0.53 | 0.75 | 30 | empty |
| 3 | 56 | 0.50 | 0.87 | 22 | empty |
| 4 | 104 | 0.36 | 0.74 | 27 | empty |
| 5 | 72 | 0.32 | 0.75 | 19 | FRU |
Interfaces
3 interfaces between chains.
- B–C · 1701 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 795 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3SO3 · Structures of Fab-Protease Complexes Reveal a Highly Specific Non-Canonical Mechanism of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Y6 · AlphaFold monomer V2.0 prediction for suppressor of tumorigenicity 14 protein (Q9Y5Y6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y5Y6
- Elsewhere: RCSB PDB 3SO3 · PDBe 3SO3 · UniProt Q9Y5Y6
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