MolNFT v2 · #141688 · protein
Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM alpha-cyclodextrin
5YNE · PulA protein: “Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM alpha-cyclodextrin”. X-ray diffraction at 2.199, 2 ligands (GLC, CA), 7 pockets (best druggability 0.61). MolNFT v2 #141688 on GenesisL1: 3D…
- PDB
- 5YNE
- Type
- protein
- Length
- 1,054 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.199
- Source
- Klebsiella pneumoniae
- Molecule
- PulA protein
- UniProt
- W9BQ28
- Ligands
- GLC, CA
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.199 · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PulA protein | protein | 1054 | 28% helix, 23% strand | W9BQ28 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A
- CA · Calcium ion · metal · 5 copies · chains A
- GOL · Glycerol · additive · 6 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.61 | 0.81 | 32 | empty |
| 2 | 333 | 0.58 | 0.77 | 43 | GLC, GOL |
| 3 | 167 | 0.50 | 0.78 | 28 | empty |
| 4 | 153 | 0.46 | 0.76 | 24 | empty |
| 5 | 78 | 0.35 | 0.76 | 17 | GOL |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5YNE · Crystal structure of pullulanase from klebsiella pneumoniae complex at 10 mm… · 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 W9BQ28
- Elsewhere: RCSB PDB 5YNE · PDBe 5YNE · UniProt W9BQ28
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