MolNFT v1 · #18450 · protein
X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and the third domain of the turkey ovomucoid inhibitor
1PPF: “X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and the third domain of the…”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.55). MolNFT v1 #18450 on GenesisL1: 3D…
- PDB
- 1PPF
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human leukocyte elastase; Turkey ovomucoid inhibitor (OMTKY3)
- EC
- 3.4.21.37
- UniProt
- P08246, P01004
- Ligands
- NAG, MAN, BMA, FUC, GAL, GLC
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 35% 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 | Turkey ovomucoid inhibitor (OMTKY3) | protein | 56 | 18% helix, 21% strand | P01004 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E
- GAL · beta-D-galactopyranose · sugar
- GLC · alpha-D-glucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.55 | 0.76 | 32 | empty |
| 2 | 90 | 0.51 | 0.83 | 18 | empty |
| 3 | 128 | 0.42 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- E–I · 685 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1PPF · X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and the… · 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
- Every structure of UniProt P01004
- Elsewhere: RCSB PDB 1PPF · PDBe 1PPF · UniProt P08246 · UniProt P01004
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