MolNFT v1 · #109364 · protein
Porcine pancreatic alpha-amylase in complex with helianthamide, a novel proteinaceous inhibitor
4X0N: “Porcine pancreatic alpha-amylase in complex with helianthamide, a novel proteinaceous inhibitor”. X-ray diffraction, 2 ligands (CA, CL), 6 pockets (best druggability 0.63). MolNFT v1 #109364 on GenesisL1: 3D structure, binding sites…
- PDB
- 4X0N
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase; Helianthamide
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- CA, CL
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
| B | Helianthamide | protein | 44 | 7% helix, 41% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.63 | 0.82 | 37 | empty |
| 2 | 148 | 0.52 | 0.80 | 31 | GOL |
| 3 | 54 | 0.36 | 0.79 | 11 | empty |
| 4 | 73 | 0.36 | 0.78 | 22 | empty |
| 5 | 70 | 0.33 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1072 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 4X0N · Porcine pancreatic alpha-amylase in complex with helianthamide, a novel proteinaceous… · the same entry in another collection · chain A against A, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00690
- Elsewhere: RCSB PDB 4X0N · PDBe 4X0N · UniProt P00690
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