MolNFT v1 · #74056 · protein
Structures of human pancreatic alpha-amylase in complex with acarviostatin IV03
3OLI: “Structures of human pancreatic alpha-amylase in complex with acarviostatin IV03”. X-ray diffraction, 8 ligands (G6D, HSD, PCA), 4 pockets (best druggability 0.59). MolNFT v1 #74056 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3OLI
- Type
- protein
- Length
- 495 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
- G6D, HSD, PCA, GLC, BGC, CA, CL, SO4
- 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 | 495 | 28% helix, 24% strand | P04746 |
Ligands and binding sites
- G6D · alpha-D-quinovopyranose · ligand · 2 copies · chains A
- HSD · (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol · ligand · 2 copies · chains A
- PCA · Pyroglutamic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · 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 | 232 | 0.59 | 0.80 | 25 | GLC, G6D, HSD |
| 2 | 107 | 0.38 | 0.75 | 19 | empty |
| 3 | 73 | 0.37 | 0.78 | 18 | empty |
| 4 | 67 | 0.32 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3OLI · Structures of human pancreatic alpha-amylase in complex with acarviostatin IV03 · 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 3OLI · PDBe 3OLI · UniProt P04746
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