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The refined 2.3 ångströms crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor
Analyse The refined 2.3 ångströms crystal structure of human leukocyte elastase in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPG
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human leukocyte elastase; Meo-succinyl-ala-ala-pro-val chloromethylketone
- EC
- 3.4.21.37
- UniProt
- P08246
- Ligands
- HMB, NAG, BMA, MAN, FUC, GAL, NDG, GLC, 0QE
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Human leukocyte elastase (EC 3.4.21.37) | protein | 218 | 8% helix, 39% strand | P08246 |
| I | Meo-succinyl-ala-ala-pro-val chloromethylketone | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- HMB · (4S)-4-hydroxy-4-methoxybutanoic acid · ligand · chains E, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E
- GAL · beta-D-galactopyranose · sugar
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains E
- GLC · alpha-D-glucopyranose · sugar · chains E
- 0QE · Chloromethane · ion · chains E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.46 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- E–I · 306 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan, 1 covalent, 1 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 1PPG · The refined 2.3 angstroms crystal structure of human leukocyte elastase in a complex with… · the same entry in another collection · chain E against E, TM-score 1.00
- P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · a predicted model of the same protein · chain E 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 1PPG · PDBe 1PPG · UniProt P08246
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