Research workbench
Crystal structure of human neutrophil elastase (hne) in complex with the 3-oxo-beta-sultam inhibitor LMC249
Analyse Crystal structure of human neutrophil elastase (hne) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMA
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil elastase
- EC
- 3.4.21.37
- UniProt
- P08246
- Ligands
- LKK, NAG, FUC, BR
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutrophil elastase (EC 3.4.21.37) | protein | 218 | 8% helix, 39% strand | P08246 |
| B | Neutrophil elastase (EC 3.4.21.37) | protein | 214 | 8% helix, 41% strand | P08246 |
Ligands and binding sites
- LKK · 3-[[1-[(4-bromophenyl)methyl]-1,2,3-triazol-4-yl]methylcarbamoyl]pentane-3-sulfonic acid · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C
- BR · Bromide ion · ion · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C
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 | 899 | 0.75 | 0.78 | 93 | empty |
| 2 | 182 | 0.66 | 0.85 | 44 | empty |
| 3 | 53 | 0.47 | 0.86 | 17 | empty |
| 4 | 55 | 0.47 | 0.85 | 18 | empty |
| 5 | 51 | 0.30 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 912 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 100 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6SMA · Crystal structure of Human Neutrophil Elastase (HNE) in complex with the… · 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 B 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 6SMA · PDBe 6SMA · UniProt P08246
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