Research workbench
Crystal structure of SdgB (complexed with phosphate ions)
Analyse Crystal structure of SdgB (complexed with phosphate ions) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EC7
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Staphylococcus aureus (strain USA300)
- Molecule
- Glycosyl transferase, group 1 family protein
- UniProt
- A0A0H2XGN0
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, group 1 family protein | protein | 496 | 30% helix, 27% strand | A0A0H2XGN0 |
| B | Glycosyl transferase, group 1 family protein | protein | 494 | 30% helix, 26% strand | A0A0H2XGN0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.77 | 0.82 | 64 | PO4 |
| 2 | 623 | 0.76 | 0.82 | 70 | PO4 |
| 3 | 780 | 0.67 | 0.74 | 66 | empty |
| 4 | 73 | 0.41 | 0.79 | 15 | empty |
| 5 | 83 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 7EC7 · Crystal structure of sdgb (complexed with phosphate ions) · 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 A0A0H2XGN0
- Elsewhere: RCSB PDB 7EC7 · PDBe 7EC7 · UniProt A0A0H2XGN0
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