MolNFT v1 · #127606 · protein
Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus
5N1J · Peptidoglycan N-acetylglucosamine deacetylase: “Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.81). MolNFT v1 #127606 on GenesisL1…
- PDB
- 5N1J
- Type
- protein
- Length
- 824 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
- ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 206 | 46% helix, 17% strand | Q81EJ6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.82 | 82 | ZN, ACT |
| 2 | 1126 | 0.78 | 0.80 | 101 | ZN, ACT, EDO |
| 3 | 66 | 0.33 | 0.76 | 13 | EDO |
| 4 | 54 | 0.28 | 0.75 | 12 | EDO |
| 5 | 53 | 0.25 | 0.72 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–C · 528 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 524 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 461 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 455 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5N1J · Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus · 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 5N1J · PDBe 5N1J · UniProt Q81EJ6
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