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Structure of a (CA,ZN)-dependent alpha-amylase from the hyperthermophilic archaeon pyrococcus woesei
Analyse Structure of a (CA,ZN)-dependent alpha-amylase from the hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MXD
- Type
- protein
- Length
- 435 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha amylase
- EC
- 3.2.1.1
- UniProt
- O08452
- Ligands
- AC1, GLC, ZN, CA
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha amylase (EC 3.2.1.1) | protein | 435 | 30% helix, 23% strand | O08452 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 4 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 9 copies · chains A
- ZN · Zinc ion · metal · 6 copies · chains A
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.40 | 0.77 | 21 | GLC, AC1 |
| 2 | 75 | 0.35 | 0.76 | 12 | AC1, ZN |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1MXD · Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon… · 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 O08452
- Elsewhere: RCSB PDB 1MXD · PDBe 1MXD · UniProt O08452
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