Research workbench
Crystal structure of putative aspartate racemase from salmonella typhimurium complexed with sulfate and potassium
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
- 5EVC
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aspartate racemase
- UniProt
- Q8ZJZ9
- Ligands
- K, SO4, CL, F
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aspartate racemase | protein | 237 | 52% helix, 13% strand | Q8ZJZ9 |
| B | Putative aspartate racemase | protein | 238 | 52% helix, 12% strand | Q8ZJZ9 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- F · Fluoride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.45 | 0.77 | 25 | K |
| 2 | 165 | 0.45 | 0.75 | 28 | K |
| 3 | 95 | 0.37 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1555 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5EVC · Crystal structure of putative aspartate racemase from Salmonella Typhimurium complexed… · 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 5EVC · PDBe 5EVC · UniProt Q8ZJZ9
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