Research workbench
Structure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor FR130180 determined by neutron crystallography
Analyse Structure of porcine pancreatic elastase complexed with a potent peptidyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HGN
- Type
- protein
- Length
- 240 residues
- Chains
- 1
- Method
- neutron diffraction; x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elastase-1
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- FRW, CA, SO4
- Pockets
- 3 · best druggability 0.56
Structure
neutron diffraction; x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elastase-1 (EC 3.4.21.36) | protein | 240 | 11% helix, 38% strand | P00772 |
Ligands and binding sites
- FRW · 4-[[(2S)-3-methyl-1-oxo-1-[(2S)-2-[[(3S)-1,1,1-trifluoro-4-methyl-2-oxo-pentan-3-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamoyl]benzoic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.56 | 0.90 | 18 | empty |
| 2 | 94 | 0.37 | 0.75 | 22 | FRW |
| 3 | 60 | 0.33 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3HGN · Structure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P00772 · AlphaFold monomer V2.0 prediction for chymotrypsin-like elastase family member 1 (P00772) · 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 P00772
- Elsewhere: RCSB PDB 3HGN · PDBe 3HGN · UniProt P00772
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