MolNFT v1 · #35359 · protein
Crystal structure of pullulanase type I from bacillus subtilis str. 168 complexed with alpha-cyclodextrin
2E8Z · Amyx protein: “Crystal structure of pullulanase type I from bacillus subtilis str. 168 complexed with alpha-cyclodextrin”. X-ray diffraction, 2 ligands (GLC, CA), 14 pockets (best druggability 0.75). MolNFT v1 #35359 on GenesisL1…
- PDB
- 2E8Z
- Type
- protein
- Length
- 1,424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyx protein
- EC
- 3.2.1.41
- UniProt
- O34587
- Ligands
- GLC, CA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amyx protein (EC 3.2.1.41) | protein | 712 | 28% helix, 28% strand | O34587 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.75 | 0.78 | 89 | empty |
| 2 | 55 | 0.65 | 0.94 | 19 | GOL |
| 3 | 221 | 0.57 | 0.79 | 33 | empty |
| 4 | 234 | 0.56 | 0.78 | 37 | GLC |
| 5 | 230 | 0.51 | 0.76 | 29 | GLC |
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2E8Z · Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with… · 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 O34587
- Elsewhere: RCSB PDB 2E8Z · PDBe 2E8Z · UniProt O34587
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