Research workbench
Recombinant medaka fish alpha-amylase expressed in yeast pichia pastoris
Analyse Recombinant medaka fish alpha-amylase expressed in yeast pichia pastoris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VM5
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase
- Ligands
- CA, CL
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase | protein | 499 | 28% helix, 23% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.59 | 0.77 | 32 | empty |
| 2 | 59 | 0.34 | 0.78 | 19 | empty |
| 3 | 62 | 0.31 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3VM5 · Recombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris · 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
- Elsewhere: RCSB PDB 3VM5 · PDBe 3VM5
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