Research workbench
Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa
Analyse Crystal structure of the catalytic domain of beta-amylase from paenibacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VOC
- Type
- protein
- Length
- 416 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BETA/ALPHA-amylase
- EC
- 3.2.1.2
- UniProt
- P21543
- Ligands
- CA, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BETA/ALPHA-amylase (EC 3.2.1.2) | protein | 416 | 43% helix, 13% strand | P21543 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.68 | 0.78 | 42 | empty |
| 2 | 89 | 0.56 | 0.86 | 20 | empty |
| 3 | 59 | 0.32 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3VOC · Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa · the same entry in another collection · chain A against A, TM-score 1.00
- P21543 · AlphaFold monomer V2.0 prediction for BETA/ALPHA-amylase (P21543) · 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 P21543
- Elsewhere: RCSB PDB 3VOC · PDBe 3VOC · UniProt P21543
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