MolNFT v1 · #128033 · protein
Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with acetazolamide
5NEK · Peptidoglycan N-acetylglucosamine deacetylase: “Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with acetazolamide”. X-ray diffraction, 2 ligands (AZM, ZN), 6 pockets (best druggability…
- 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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