Research workbench
Extracellular proteins of staphylococcus aureus inhibit the neutrophil serine proteases
Analyse Extracellular proteins of staphylococcus aureus inhibit the neutrophil serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZL
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil elastase; Uncharacterized protein
- EC
- 3.4.21.37
- UniProt
- P08246, Q99S64
- Ligands
- NAG, BMA, FUL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil elastase (EC 3.4.21.37) | protein | 218 | 8% helix, 40% strand | P08246 |
| B | Uncharacterized protein | protein | 96 | 26% helix, 41% strand | Q99S64 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUL · beta-L-fucopyranose · sugar · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.54 | 0.79 | 24 | empty |
| 2 | 74 | 0.52 | 0.85 | 18 | empty |
| 3 | 133 | 0.51 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 897 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4NZL · Extracellular proteins of Staphylococcus aureus inhibit the neutrophil serine proteases · the same entry in another collection · chain A against A, TM-score 1.00
- P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · 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 P08246
- Every structure of UniProt Q99S64
- Elsewhere: RCSB PDB 4NZL · PDBe 4NZL · UniProt P08246 · UniProt Q99S64
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