Research workbench
Crystal structure of thermoactinomyces vulgaris R-47 alpha-amylase 1 (tvai) mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide
Analyse Crystal structure of thermoactinomyces vulgaris R-47 alpha-amylase 1 (tvai)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D0H
- Type
- protein
- Length
- 637 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase I
- EC
- 3.2.1.1
- UniProt
- Q60053
- Ligands
- GLC, CA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase I (EC 3.2.1.1) | protein | 637 | 25% helix, 27% strand | Q60053 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.69 | 0.84 | 40 | empty |
| 2 | 253 | 0.56 | 0.77 | 33 | GLC |
| 3 | 55 | 0.43 | 0.83 | 17 | empty |
| 4 | 59 | 0.30 | 0.75 | 20 | empty |
Compared structures
- 2D0H · Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- Q60053 · AlphaFold monomer V2.0 prediction for neopullulanase 1 (Q60053) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q60053
- Elsewhere: RCSB PDB 2D0H · PDBe 2D0H · UniProt Q60053
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