Research workbench
Endo-polygalacturonase II from aspergillus niger
Analyse Endo-polygalacturonase II from aspergillus niger in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CZF
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polygalacturonase II
- EC
- 3.2.1.15
- UniProt
- P26214
- Ligands
- NAG, ZN
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polygalacturonase II (EC 3.2.1.15) | protein | 335 | 5% helix, 54% strand | P26214 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.42 | 0.76 | 28 | empty |
| 2 | 130 | 0.39 | 0.75 | 31 | empty |
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
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 P26214
- Elsewhere: RCSB PDB 1CZF · PDBe 1CZF · UniProt P26214
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