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Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.
Analyse Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G1Y
- Type
- protein
- Length
- 991 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.43
- Source
- Streptococcus pneumoniae TIGR4
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- A0A0H2US33
- Ligands
- PLP, MLT, NA, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.43 · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine synthase (EC 4.2.3.1) | protein | 496 | 46% helix, 16% strand | A0A0H2US33 |
| B | Threonine synthase (EC 4.2.3.1) | protein | 495 | 46% helix, 16% strand | A0A0H2US33 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MLT · D-malate · ligand · chains A
- NA · Sodium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.77 | 0.79 | 100 | PLP, GOL, MLT |
| 2 | 1111 | 0.77 | 0.79 | 104 | PLP, GOL |
| 3 | 615 | 0.70 | 0.79 | 56 | empty |
| 4 | 588 | 0.69 | 0.78 | 55 | GOL |
| 5 | 225 | 0.48 | 0.75 | 34 | NA |
Interfaces
1 interface between chains.
- A–B · 506 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 modified, 2 cofactor (engineered, pyridoxal phosphate Schiff base).
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 A0A0H2US33
- Elsewhere: RCSB PDB 8G1Y · PDBe 8G1Y · UniProt A0A0H2US33
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