Research workbench
Crystal structure of pullulanase from klebsiella pneumoniae complex at 1 mm gamma-cyclodextrin
Analyse Crystal structure of pullulanase from klebsiella pneumoniae complex at 1 mm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YND
- Type
- protein
- Length
- 1,055 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF3372 domain-containing protein
- UniProt
- W9BQ28
- Ligands
- GLC, CA
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DUF3372 domain-containing protein | protein | 1055 | 28% helix, 23% strand | W9BQ28 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · 5 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.62 | 0.77 | 47 | PEG, GOL |
| 2 | 197 | 0.62 | 0.82 | 40 | empty |
| 3 | 146 | 0.47 | 0.78 | 24 | empty |
| 4 | 136 | 0.42 | 0.75 | 21 | empty |
| 5 | 91 | 0.38 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5YND · Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 1 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 5YND · PDBe 5YND · UniProt W9BQ28
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