Research workbench
Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with acetazolamide
Analyse Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NEK
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- Q81EJ6
- Ligands
- AZM, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 205 | 45% helix, 17% strand | Q81EJ6 |
| B, D | Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 206 | 47% helix, 16% strand | Q81EJ6 |
Ligands and binding sites
- AZM · 5-acetamido-1,3,4-thiadiazole-2-sulfonamide · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.79 | 0.80 | 95 | ZN, ACT, AZM |
| 2 | 1173 | 0.78 | 0.79 | 98 | ZN, AZM, ACT |
| 3 | 149 | 0.41 | 0.74 | 20 | empty |
| 4 | 50 | 0.34 | 0.78 | 13 | empty |
| 5 | 76 | 0.34 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 515 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 463 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 459 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5NEK · Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81EJ6 · AlphaFold monomer V2.0 prediction for peptidoglycan-N- acetylglucosamine deacetylase… · a predicted model of the same protein · 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 Q81EJ6
- Elsewhere: RCSB PDB 5NEK · PDBe 5NEK · UniProt Q81EJ6
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