MolNFT v1 · #51782 · protein
The three-dimensional structure of the N-acetylglucosamine-6- phosphate deacetylase from bacillus subtilis
2VHL · N-acetylglucosamine-6-phosphate deacetylase: “The three-dimensional structure of the N-acetylglucosamine-6- phosphate deacetylase from bacillus subtilis”. X-ray diffraction, 2 ligands (GLP, FE), 4 pockets (best druggability 0.68).…
- PDB
- 2VHL
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-6-phosphate deacetylase
- EC
- 3.5.1.25
- UniProt
- O34450
- Ligands
- GLP, FE
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 392 | 31% helix, 29% strand | O34450 |
| B | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 393 | 31% helix, 30% strand | O34450 |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.68 | 0.75 | 59 | empty |
| 2 | 81 | 0.53 | 0.85 | 20 | GLP, FE |
| 3 | 76 | 0.51 | 0.85 | 21 | GLP, FE |
| 4 | 85 | 0.33 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VHL · The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- O34450 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-6-phosphate deacetylase (O34450) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O34450
- Elsewhere: RCSB PDB 2VHL · PDBe 2VHL · UniProt O34450
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