Research workbench
Crystal structure of H119A mutant of ydaa (universal stress protein E) from salmonella typhimurium
Analyse Crystal structure of H119A mutant of ydaa (universal stress protein E) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R2K
- Type
- protein
- Length
- 311 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Universal stress protein E
- UniProt
- Q8ZP84
- Ligands
- OXD, SO4
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Universal stress protein E | protein | 311 | 43% helix, 20% strand | Q8ZP84 |
Ligands and binding sites
- OXD · Oxalic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 16 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.65 | 0.90 | 26 | EDO |
| 2 | 83 | 0.50 | 0.83 | 20 | empty |
| 3 | 123 | 0.44 | 0.76 | 21 | SO4 |
| 4 | 86 | 0.37 | 0.76 | 16 | empty |
| 5 | 91 | 0.36 | 0.75 | 20 | EDO |
Compared structures
- 4R2K · Crystal structure of H119A mutant of YdaA (Universal Stress Protein E) from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZP84 · AlphaFold monomer V2.0 prediction for universal stress protein E (Q8ZP84) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8ZP84
- Elsewhere: RCSB PDB 4R2K · PDBe 4R2K · UniProt Q8ZP84
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