Research workbench
Crystal structure of barley beta-amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside
Analyse Crystal structure of barley beta-amylase complexed with 3,4- epoxybutyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XGI
- Type
- protein
- Length
- 487 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-amylase
- EC
- 3.2.1.2
- UniProt
- P16098
- Ligands
- J5B, EBQ
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-amylase (EC 3.2.1.2) | protein | 487 | 38% helix, 12% strand | P16098 |
Ligands and binding sites
- J5B · (3R)-3-hydroxybutyl alpha-D-glucopyranoside · ligand · chains A
- EBQ · (3S)-3-hydroxybutyl alpha-D-glucopyranoside · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.73 | 0.81 | 51 | J5B, EBQ |
| 2 | 162 | 0.58 | 0.82 | 39 | empty |
| 3 | 54 | 0.34 | 0.78 | 14 | empty |
| 4 | 56 | 0.30 | 0.76 | 19 | empty |
| 5 | 53 | 0.29 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 P16098
- Elsewhere: RCSB PDB 2XGI · PDBe 2XGI · UniProt P16098
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.