Research workbench
Crystallographic analysis of the inhibition of porcine pancreatic elastase by a peptidyl boronic acid: structure of a reaction intermediate
Analyse Crystallographic analysis of the inhibition of porcine pancreatic elastase by a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EST
- Type
- protein
- Length
- 240 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elastase
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- 0P2, CA, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Elastase (EC 3.4.21.36) | protein | 240 | 12% helix, 38% strand | P00772 |
Ligands and binding sites
- 0P2 · N~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide · ligand · chains E
- CA · Calcium ion · metal · chains E
- SO4 · Sulfate ion · ion · chains E
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 | 53 | 0.55 | 0.89 | 17 | empty |
| 2 | 90 | 0.36 | 0.75 | 27 | 0P2 |
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5EST · Crystallographic analysis of the inhibition of porcine pancreatic elastase by a peptidyl… · the same entry in another collection · chain E against E, 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 E 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 5EST · PDBe 5EST · UniProt P00772
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