MolNFT v1 · #32844 · protein
Crystal structure of threonine synthase from arabidopsis thaliana in complex with its cofactor pyridoxal phosphate
2C2G: “Crystal structure of threonine synthase from arabidopsis thaliana in complex with its cofactor pyridoxal…”. X-ray diffraction, 1 ligand (PLP), 12 pockets (best druggability 0.82). MolNFT v1 #32844 on GenesisL1: 3D structure, binding…
- 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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