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The crystal structure of an universal stress protein uspa family protein from lactobacillus plantarum WCFS1
Analyse The crystal structure of an universal stress protein uspa family protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FG9
- Type
- protein
- Length
- 893 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein of universal stress protein uspa family
- UniProt
- Q88RY8
- Ligands
- MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein of universal stress protein uspa family | protein | 156 | 46% helix, 18% strand | Q88RY8 |
| B | Protein of universal stress protein uspa family | protein | 146 | 46% helix, 21% strand | Q88RY8 |
| C, E | Protein of universal stress protein uspa family | protein | 150 | 42% helix, 20% strand | Q88RY8 |
| D | Protein of universal stress protein uspa family | protein | 150 | 46% helix, 20% strand | Q88RY8 |
| F | Protein of universal stress protein uspa family | protein | 141 | 47% helix, 21% strand | Q88RY8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, E, B, C, D, F
- FMT · Formic acid · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.98 | 15 | empty |
| 2 | 450 | 0.71 | 0.81 | 64 | MG |
| 3 | 535 | 0.71 | 0.80 | 62 | FMT, MG |
| 4 | 76 | 0.40 | 0.79 | 15 | empty |
| 5 | 59 | 0.34 | 0.77 | 16 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1982 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 1779 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1760 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 511 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 487 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3FG9 · The crystal structure of an universal stress protein UspA family protein from… · 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 Q88RY8
- Elsewhere: RCSB PDB 3FG9 · PDBe 3FG9 · UniProt Q88RY8
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