Research workbench
Crystal Structure of SPY
Analyse Crystal Structure of SPY in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O39
- Type
- protein
- Length
- 192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.599
- Source
- Escherichia coli
- Molecule
- Periplasmic protein related to spheroblast formation
- UniProt
- Q8XDZ4
- Ligands
- CD
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.599 · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic protein related to spheroblast formation | protein | 96 | 68% helix, 0% strand | Q8XDZ4 |
Ligands and binding sites
- CD · Cadmium ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.63 | 0.75 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 1614 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
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 Q8XDZ4
- Elsewhere: RCSB PDB 3O39 · PDBe 3O39 · UniProt Q8XDZ4
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