MolNFT v1 · #20774 · protein
Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with acarbose
1RPK · Alpha-amylase type 1 isozyme: “Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with acarbose”. X-ray diffraction, 3 ligands (DAF, GLC, CA), 1 pocket (best druggability 0.42). MolNFT v1 #20774 on GenesisL1: 3D…
- PDB
- 1RPK
- Type
- protein
- Length
- 404 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase type 1 isozyme
- EC
- 3.2.1.1
- UniProt
- P00693
- Ligands
- DAF, GLC, CA
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase type 1 isozyme (EC 3.2.1.1) | protein | 404 | 34% helix, 19% strand | P00693 |
Ligands and binding sites
- DAF · 4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose · ligand · 3 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.42 | 0.75 | 19 | DAF |
Compared structures
- 1RPK · Crystal structure of barley alpha-amylase isozyme 1 (amy1) in complex with acarbose · the same entry in another collection · chain A against A, TM-score 1.00
- P00693 · AlphaFold monomer V2.0 prediction for alpha-amylase type a isozyme (P00693) · 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 P00693
- Elsewhere: RCSB PDB 1RPK · PDBe 1RPK · UniProt P00693
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