Research workbench
Crystal structure of putative aspartate racemase from salmonella typhimurium complexed with succinate
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
- 3S7Z
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aspartate racemase
- UniProt
- Q8ZJZ9
- Ligands
- GLC, FRU, MG
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aspartate racemase | protein | 233 | 52% helix, 12% strand | Q8ZJZ9 |
| B | Putative aspartate racemase | protein | 235 | 53% helix, 13% strand | Q8ZJZ9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains B
- FRU · beta-D-fructofuranose · sugar · chains B
- MG · Magnesium ion · metal · chains B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.51 | 0.80 | 25 | empty |
| 2 | 139 | 0.46 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1447 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3S7Z · 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 3S7Z · PDBe 3S7Z · UniProt Q8ZJZ9
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