MolNFT v1 · #118222 · protein
Crystal structure of putative aspartate racemase from salmonella typhimurium complexed with sulfate and potassium
5EVC: “Crystal structure of putative aspartate racemase from salmonella typhimurium complexed with sulfate and…”. X-ray diffraction, 4 ligands (K, SO4, CL), 3 pockets (best druggability 0.45). MolNFT v1 #118222 on GenesisL1: 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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