MolNFT v1 · #124428 · protein
Selective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide piha from mRNA display
5KEZ · Pancreatic alpha-amylase: “Selective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide…”. X-ray diffraction, 4 ligands (ACE, CA, NH2), 4 pockets (best druggability 0.49). MolNFT v1…
- 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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