MolNFT v1 · #105358 · protein
Crystal structure of ydaa (universal stress protein E) from salmonella typhimurium
4R2J: “Crystal structure of ydaa (universal stress protein E) from salmonella typhimurium”. X-ray diffraction, 3 ligands (GLC, ZN, PO4), 4 pockets (best druggability 0.60). MolNFT v1 #105358 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4R2J
- Type
- protein
- Length
- 285 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Universal stress protein E
- UniProt
- Q8ZP84
- Ligands
- GLC, ZN, PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Universal stress protein E | protein | 285 | 45% helix, 22% strand | Q8ZP84 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.60 | 0.84 | 25 | empty |
| 2 | 214 | 0.58 | 0.80 | 35 | empty |
| 3 | 68 | 0.36 | 0.77 | 17 | empty |
| 4 | 64 | 0.35 | 0.77 | 16 | empty |
Compared structures
- 4R2J · Crystal structure of YdaA (Universal Stress Protein E) from Salmonella typhimurium · 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 0.98
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 4R2J · PDBe 4R2J · UniProt Q8ZP84
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