Research workbench
X-ray crystal structure of plp bound threonine synthase from brucella melitensis
Analyse X-ray crystal structure of plp bound threonine synthase from brucella melitensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F4F
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- Q8YFS0
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Threonine synthase (EC 4.2.3.1) | protein | 464 | 48% helix, 17% strand | Q8YFS0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.71 | 0.86 | 43 | PLP |
| 2 | 257 | 0.71 | 0.86 | 47 | PLP |
| 3 | 273 | 0.65 | 0.82 | 37 | empty |
| 4 | 90 | 0.57 | 0.86 | 20 | empty |
| 5 | 65 | 0.51 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4F4F · X-Ray crystal structure of PLP bound Threonine synthase from Brucella melitensis · 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 Q8YFS0
- Elsewhere: RCSB PDB 4F4F · PDBe 4F4F · UniProt Q8YFS0
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