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Human neutrophil elastase in-complex with ecotin peptide
Analyse Human neutrophil elastase in-complex with ecotin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHU
- Type
- protein
- Length
- 904 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil elastase; Ecotin peptide
- EC
- 3.4.21.37
- UniProt
- P08246
- Ligands
- NAG, FUC, BMA, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | Neutrophil elastase (EC 3.4.21.37) | protein | 218 | 8% helix, 38% strand | P08246 |
| E, F, G, H | Ecotin peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, D, C, A
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 5 copies · chains D, B, C
- GOL · Glycerol · additive · 6 copies · chains D, A, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.74 | 0.89 | 32 | empty |
| 2 | 132 | 0.71 | 0.91 | 28 | empty |
| 3 | 106 | 0.48 | 0.80 | 17 | empty |
| 4 | 72 | 0.45 | 0.82 | 19 | empty |
| 5 | 113 | 0.43 | 0.77 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 911 Ų buried · 17 hydrogen bonds · protein-protein
- D–A · 758 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 494 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 472 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
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 7WHU · PDBe 7WHU · UniProt P08246
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