Research workbench
X-ray structure of a monoclinic form of alpha amylase from aspergillus at 1.4 a resolution
Analyse X-ray structure of a monoclinic form of alpha amylase from aspergillus at 1.4 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XSJ
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- B0FZ76
- Ligands
- NAG, MAN, CA, PO4, ALA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-amylase (EC 3.2.1.1) | protein | 476 | 36% helix, 21% strand | B0FZ76 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B
- ALA · Alanine · ion · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.64 | 0.80 | 55 | empty |
| 2 | 367 | 0.62 | 0.78 | 28 | empty |
| 3 | 331 | 0.60 | 0.77 | 30 | empty |
| 4 | 159 | 0.45 | 0.75 | 31 | empty |
| 5 | 80 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XSJ · X-ray structure of a monoclinic form of alpha amylase from Aspergillus at 1.4 A resolution · the same entry in another collection · 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 B0FZ76
- Elsewhere: RCSB PDB 6XSJ · PDBe 6XSJ · UniProt B0FZ76
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.