Research workbench
Crystal structure of a polysaccharide deacetylase family protein from burkholderia pseudomallei
Analyse Crystal structure of a polysaccharide deacetylase family protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S6O
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polysaccharide deacetylase family protein
- EC
- 3.5.1.-
- UniProt
- Q3JR78
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Polysaccharide deacetylase family protein (EC 3.5.1.-) | protein | 305 | 40% helix, 15% strand | Q3JR78 |
| C | Polysaccharide deacetylase family protein (EC 3.5.1.-) | protein | 306 | 40% helix, 15% strand | Q3JR78 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.74 | 0.99 | 17 | empty |
| 2 | 57 | 0.73 | 0.99 | 17 | empty |
| 3 | 52 | 0.73 | 1.00 | 16 | empty |
| 4 | 54 | 0.72 | 0.99 | 17 | empty |
| 5 | 293 | 0.67 | 0.82 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2219 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2205 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2188 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2126 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3S6O · Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia… · 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 Q3JR78
- Elsewhere: RCSB PDB 3S6O · PDBe 3S6O · UniProt Q3JR78
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