MolNFT v1 · #127964 · protein
Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl) prop-2-enamide
5NC6 · Peptidoglycan N-acetylglucosamine deacetylase: “Crystal structure of the polysaccharide deacetylase BC1974 from bacillus cereus in complex with…”. X-ray diffraction, 2 ligands (8SQ, ZN), 5 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5NC6
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan N-acetylglucosamine deacetylase
- UniProt
- A0A0A3VTA3
- Ligands
- 8SQ, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan N-acetylglucosamine deacetylase | protein | 205 | 45% helix, 16% strand | A0A0A3VTA3 |
| B, C, D | Peptidoglycan N-acetylglucosamine deacetylase | protein | 206 | 47% helix, 16% strand | A0A0A3VTA3 |
Ligands and binding sites
- 8SQ · 3-naphthalen-1-yl-~{N}-oxidanyl-propanamide · 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
- EDO · 1,2-ethanediol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B, 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 | 91 | ACT, ZN, 8SQ |
| 2 | 1005 | 0.80 | 0.81 | 90 | 8SQ, ACT |
| 3 | 52 | 0.31 | 0.77 | 13 | empty |
| 4 | 58 | 0.29 | 0.75 | 18 | EDO |
| 5 | 50 | 0.23 | 0.72 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–D · 525 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 475 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 464 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NC6 · 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
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 A0A0A3VTA3
- Elsewhere: RCSB PDB 5NC6 · PDBe 5NC6 · UniProt A0A0A3VTA3
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