Research workbench
X-ray crystal structure of protein yonk from bacillus subtilis. northeast structural genomics consortium target SR415
Analyse X-ray crystal structure of protein yonk from bacillus subtilis. northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H4O
- Type
- protein
- Length
- 248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yonk protein
- UniProt
- O31947
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Yonk protein | protein | 62 | 10% helix, 32% strand | O31947 |
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 | 203 | 0.50 | 0.76 | 22 | empty |
| 2 | 190 | 0.48 | 0.75 | 23 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2237 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2H4O · X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- O31947 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived uncharacterized protein… · a predicted model of the same protein · chain A against A, TM-score 0.88
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 O31947
- Elsewhere: RCSB PDB 2H4O · PDBe 2H4O · UniProt O31947
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