MolNFT v1 · #62472 · protein
N-acetylglucosamine-6-phosphate deacetylase from vibrio cholerae.
3EGJ: “N-acetylglucosamine-6-phosphate deacetylase from vibrio cholerae.”. X-ray diffraction, 2 ligands (NI, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #62472 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EGJ
- Type
- protein
- Length
- 740 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
- O32445
- Ligands
- NI, SO4
- Pockets
- 4 · best druggability 0.75
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 | 379 | 30% helix, 27% strand | O32445 |
| B | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 361 | 32% helix, 30% strand | O32445 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.75 | 0.79 | 63 | empty |
| 2 | 109 | 0.50 | 0.81 | 22 | empty |
| 3 | 71 | 0.50 | 0.84 | 19 | empty |
| 4 | 86 | 0.32 | 0.74 | 22 | NI |
Interfaces
1 interface between chains.
- A–B · 370 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3EGJ · N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae. · the same entry in another collection · chain A against A, TM-score 1.00
- O32445 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-6-phosphate deacetylase (O32445) · 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 O32445
- Elsewhere: RCSB PDB 3EGJ · PDBe 3EGJ · UniProt O32445
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