Research workbench
Crystal structure of porcine pancreatic elastase (ppe) in complex with the novel inhibitor JM102
Analyse Crystal structure of porcine pancreatic elastase (ppe) 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
- 4YM9
- Type
- protein
- Length
- 240 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymotrypsin-like elastase family member 1
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- 4E4, NA, SO4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chymotrypsin-like elastase family member 1 (EC 3.4.21.36) | protein | 240 | 11% helix, 38% strand | P00772 |
Ligands and binding sites
- 4E4 · 2-ethyl-2-(hydroxymethyl)-N-(6-methylpyridin-3-yl)butanamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- ACT · Acetate ion · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.60 | 0.91 | 18 | empty |
| 2 | 67 | 0.32 | 0.76 | 20 | 4E4, SO4 |
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4YM9 · Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the novel… · 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 1.00
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 4YM9 · PDBe 4YM9 · UniProt P00772
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.