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Crystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium
Analyse Crystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S81
- Type
- protein
- Length
- 944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.796
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium
- Molecule
- Putative aspartate racemase
- UniProt
- Q8ZJZ9
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.796 · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aspartate racemase | protein | 232 | 52% helix, 13% strand | Q8ZJZ9 |
| B | Putative aspartate racemase | protein | 240 | 51% helix, 13% strand | Q8ZJZ9 |
| C | Putative aspartate racemase | protein | 239 | 51% helix, 13% strand | Q8ZJZ9 |
| D | Putative aspartate racemase | protein | 233 | 52% helix, 12% strand | Q8ZJZ9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.72 | 0.81 | 69 | empty |
| 2 | 383 | 0.71 | 0.83 | 42 | empty |
| 3 | 278 | 0.63 | 0.80 | 30 | empty |
| 4 | 269 | 0.61 | 0.79 | 26 | empty |
| 5 | 232 | 0.49 | 0.75 | 36 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1470 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1469 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 903 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 323 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3S81 · Crystal structure of putative aspartate racemase from salmonella typhimurium · 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 Q8ZJZ9
- Elsewhere: RCSB PDB 3S81 · PDBe 3S81 · UniProt Q8ZJZ9
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