Research workbench
N,N'-diacetylchitobiose deacetylase from pyrococcus horikoshii
Analyse N,N'-diacetylchitobiose deacetylase from pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WL3
- Type
- protein
- Length
- 799 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0499
- UniProt
- O58235
- Ligands
- ZN, PO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative uncharacterized protein PH0499 | protein | 267 | 43% helix, 15% strand | O58235 |
| B | Putative uncharacterized protein PH0499 | protein | 265 | 43% helix, 15% strand | O58235 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.82 | 55 | PO4 |
| 2 | 846 | 0.79 | 0.82 | 59 | PO4, GOL |
| 3 | 874 | 0.78 | 0.81 | 59 | PO4, GOL |
| 4 | 824 | 0.77 | 0.81 | 56 | ZN, PO4 |
| 5 | 68 | 0.42 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1901 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1871 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1779 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3WL3 · N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii · 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 O58235
- Elsewhere: RCSB PDB 3WL3 · PDBe 3WL3 · UniProt O58235
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