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Crystal structure of an uncharacterized protein (yobk, BSU18990) from bacillus subtilis at 1.30 a resolution
Analyse Crystal structure of an uncharacterized protein (yobk, BSU18990) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PRV
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein yobk
- UniProt
- O34596
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein yobk | protein | 153 | 42% helix, 22% strand | O34596 |
| B | Uncharacterized protein yobk | protein | 152 | 43% helix, 23% strand | O34596 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.76 | 0.85 | 50 | EDO, SO4 |
| 2 | 52 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2PRV · Crystal structure of an uncharacterized protein (yobk, bsu18990) from bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- O34596 · AlphaFold monomer V2.0 prediction for antitoxin yobk (O34596) · a predicted model of the same protein · chain B 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 O34596
- Elsewhere: RCSB PDB 2PRV · PDBe 2PRV · UniProt O34596
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