MolNFT v1 · #105359 · protein
Crystal structure of H119A mutant of ydaa (universal stress protein E) from salmonella typhimurium
4R2K: “Crystal structure of H119A mutant of ydaa (universal stress protein E) from salmonella typhimurium”. X-ray diffraction, 2 ligands (OXD, SO4), 8 pockets (best druggability 0.65). MolNFT v1 #105359 on GenesisL1: 3D structure, binding…
- 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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