Research workbench
Crystal structure of threonine synthase from arabidopsis thaliana in complex with its cofactor pyridoxal phosphate
Analyse Crystal structure of threonine synthase from arabidopsis thaliana in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C2G
- Type
- protein
- Length
- 885 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- Q9S7B5
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine synthase (EC 4.2.3.1) | protein | 448 | 39% helix, 15% strand | Q9S7B5 |
| B | Threonine synthase (EC 4.2.3.1) | protein | 437 | 41% helix, 15% strand | Q9S7B5 |
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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.82 | 0.87 | 86 | empty |
| 2 | 453 | 0.64 | 0.77 | 64 | PLP |
| 3 | 268 | 0.60 | 0.79 | 38 | PLP |
| 4 | 215 | 0.57 | 0.79 | 20 | empty |
| 5 | 235 | 0.57 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4160 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2C2G · Crystal structure of Threonine Synthase from Arabidopsis thaliana in complex with its… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9S7B5 · AlphaFold monomer V2.0 prediction for threonine synthase 1, chloroplastic (Q9S7B5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9S7B5
- Elsewhere: RCSB PDB 2C2G · PDBe 2C2G · UniProt Q9S7B5
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