Research workbench
Structure of bacillus subtilis pdaa, a family 4 carbohydrate esterase.
Analyse Structure of bacillus subtilis pdaa, a family 4 carbohydrate esterase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W17
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable polysaccharide deacetylase pdaa
- EC
- 3.-.-.-
- UniProt
- O34928
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable polysaccharide deacetylase pdaa (EC 3.-.-.-) | protein | 235 | 43% helix, 16% strand | O34928 |
| B | Probable polysaccharide deacetylase pdaa (EC 3.-.-.-) | protein | 234 | 43% helix, 15% strand | O34928 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.49 | 0.75 | 26 | empty |
| 2 | 212 | 0.48 | 0.75 | 30 | empty |
| 3 | 84 | 0.33 | 0.74 | 16 | empty |
| 4 | 80 | 0.31 | 0.73 | 15 | empty |
| 5 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 122 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1W17 · Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. · the same entry in another collection · chain A against A, TM-score 1.00
- O34928 · AlphaFold monomer V2.0 prediction for peptidoglycan-N-acetylmuramic acid deacetylase pdaa… · a predicted model of the same protein · chain B 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 O34928
- Elsewhere: RCSB PDB 1W17 · PDBe 1W17 · UniProt O34928
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