Research workbench
Acarbose rearrangement mechanism implied by the kinetic and structural analysis of human pancreatic alpha-amylase in complex with analogues and their elongated counterparts
Analyse Acarbose rearrangement mechanism implied by the kinetic and structural analysis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XD1
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- 6SA, NAG, CA, CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase (EC 3.2.1.1) | protein | 496 | 27% helix, 24% strand | P04746 |
Ligands and binding sites
- 6SA · Acarbose derived hexasaccharide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 275 | 0.58 | 0.78 | 25 | 6SA |
| 2 | 80 | 0.37 | 0.77 | 19 | empty |
| 3 | 51 | 0.37 | 0.80 | 14 | empty |
| 4 | 88 | 0.36 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1XD1 · Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human… · 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 1XD1 · PDBe 1XD1 · UniProt P04746
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