Research workbench
Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase inhibitory fragments
Analyse Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E69
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil elastase
- EC
- 3.4.21.37
- UniProt
- P08246
- Ligands
- HVP, NAG, FUC
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Neutrophil elastase (EC 3.4.21.37) | protein | 218 | 9% helix, 39% strand | P08246 |
| D | Neutrophil elastase (EC 3.4.21.37) | protein | 215 | 8% helix, 40% strand | P08246 |
Ligands and binding sites
- HVP · 2-(fluorosulfonyl)benzene-1-sulfonic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.64 | 0.76 | 50 | empty |
| 2 | 351 | 0.56 | 0.75 | 51 | HVP |
| 3 | 211 | 0.55 | 0.78 | 44 | empty |
| 4 | 67 | 0.50 | 0.85 | 23 | empty |
| 5 | 56 | 0.49 | 0.86 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–D · 530 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 146 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan, 4 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6E69 · Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase… · the same entry in another collection · chain D against D, TM-score 1.00
- P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · a predicted model of the same protein · chain D 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 P08246
- Elsewhere: RCSB PDB 6E69 · PDBe 6E69 · UniProt P08246
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