Research workbench
X-ray crystal structure of protein yppe from bacillus subtilis. northeast structural genomics consortium target SR213.
Analyse X-ray crystal structure of protein yppe 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
- 2IM8
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yppe
- UniProt
- P50833
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein yppe | protein | 123 | 83% helix, 0% strand | P50833 |
| B | Hypothetical protein yppe | protein | 116 | 79% helix, 0% strand | P50833 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.54 | 0.77 | 40 | empty |
| 2 | 213 | 0.51 | 0.76 | 31 | empty |
| 3 | 52 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2IM8 · X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- P50833 · AlphaFold monomer V2.0 prediction for uncharacterized protein yppe (P50833) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P50833
- Elsewhere: RCSB PDB 2IM8 · PDBe 2IM8 · UniProt P50833
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