Research workbench
Crystal structure of putative polysaccharide deacetylase from mycobacterium smegmatis
Analyse Crystal structure of putative polysaccharide deacetylase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RXZ
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polysaccharide deacetylase
- UniProt
- A0R0G0
- Ligands
- ZN, CL
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polysaccharide deacetylase | protein | 286 | 47% helix, 14% strand | A0R0G0 |
| B | Polysaccharide deacetylase | protein | 286 | 48% helix, 14% strand | A0R0G0 |
| C, D | Polysaccharide deacetylase | protein | 287 | 46% helix, 15% strand | A0R0G0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.67 | 0.83 | 43 | empty |
| 2 | 306 | 0.67 | 0.82 | 37 | empty |
| 3 | 268 | 0.66 | 0.83 | 43 | empty |
| 4 | 269 | 0.65 | 0.82 | 37 | empty |
| 5 | 264 | 0.62 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1727 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1690 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1665 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3RXZ · Crystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis · 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 A0R0G0
- Elsewhere: RCSB PDB 3RXZ · PDBe 3RXZ · UniProt A0R0G0
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