Research workbench
Universal stress protein uspa from lactobacillus plantarum
Analyse Universal stress protein uspa from lactobacillus plantarum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S3T
- Type
- protein
- Length
- 1,156 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide-binding protein, universal stress protein uspa family
- UniProt
- Q88XN4
- Ligands
- ATP, CA
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Nucleotide-binding protein, universal stress protein uspa family | protein | 145 | 46% helix, 21% strand | Q88XN4 |
| B, F, G, H | Nucleotide-binding protein, universal stress protein uspa family | protein | 144 | 47% helix, 22% strand | Q88XN4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.86 | 0.88 | 72 | ATP, CA |
| 2 | 857 | 0.86 | 0.88 | 75 | ATP, CA |
| 3 | 842 | 0.85 | 0.88 | 74 | ATP, CA |
| 4 | 597 | 0.85 | 0.90 | 72 | ATP, CA |
| 5 | 334 | 0.79 | 0.89 | 43 | empty |
Interfaces
10 interfaces between chains.
- E–G · 1232 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1220 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1213 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 1213 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1009 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3S3T · Universal stress protein UspA from Lactobacillus plantarum · 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 Q88XN4
- Elsewhere: RCSB PDB 3S3T · PDBe 3S3T · UniProt Q88XN4
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