Research workbench
Selective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide piha from mRNA display
Analyse Selective and potent inhibition of the glycosidase human amylase by the short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEZ
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase; ACE-dty-pro-tyr-ser-cys-TRP-val-arg-his-NH2
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- ACE, CA, NH2, CL
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 27% helix, 24% strand | P04746 |
| B | ACE-dty-pro-tyr-ser-cys-TRP-val-arg-his-NH2 | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- NH2 · Amino group · ion · chains B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.49 | 0.83 | 23 | empty |
| 2 | 66 | 0.31 | 0.75 | 16 | empty |
| 3 | 59 | 0.31 | 0.75 | 12 | empty |
| 4 | 52 | 0.25 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent, 1 d-amino, 1 modified (disulfide, covalent ligand, D-amino acid, cyclization).
Compared structures
- 5KEZ · Selective and potent inhibition of the glycosidase human amylase by the short and… · the same entry in another collection · chain A against A, TM-score 1.00
- P04746 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P04746) · 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 P04746
- Elsewhere: RCSB PDB 5KEZ · PDBe 5KEZ · UniProt P04746
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