MolNFT v1 · #117931 · protein
Human pancreatic alpha-amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol
5EMY: “Human pancreatic alpha-amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol”. X-ray diffraction, 3 ligands (5QP, CA, CL), 4 pockets (best druggability 0.59). MolNFT v1 #117931 on GenesisL1: 3D…
- PDB
- 5EMY
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- 5QP, CA, CL
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P04746 |
Ligands and binding sites
- 5QP · (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside · ligand · chains A
- CA · Calcium ion · metal · chains A
- 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.59 | 0.80 | 25 | 5QP |
| 2 | 78 | 0.39 | 0.78 | 19 | empty |
| 3 | 58 | 0.36 | 0.79 | 12 | empty |
| 4 | 97 | 0.35 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 5EMY · Human Pancreatic Alpha-Amylase in complex with the mechanism based inactivator glucosyl… · 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 5EMY · PDBe 5EMY · UniProt P04746
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