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Crystallographic structure of arabidopsis thaliana threonine synthase complexed with pyridoxal phosphate and S-adenosylmethionine
Analyse Crystallographic structure of arabidopsis thaliana threonine synthase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C2B
- Type
- protein
- Length
- 2,617 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase 1, chloroplastic
- EC
- 4.2.3.1
- UniProt
- Q9S7B5
- Ligands
- SAM, PLP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Threonine synthase 1, chloroplastic (EC 4.2.3.1) | protein | 444 | 40% helix, 15% strand | Q9S7B5 |
| B, D | Threonine synthase 1, chloroplastic (EC 4.2.3.1) | protein | 428 | 41% helix, 15% strand | Q9S7B5 |
| C | Threonine synthase 1, chloroplastic (EC 4.2.3.1) | protein | 443 | 40% helix, 15% strand | Q9S7B5 |
| E | Threonine synthase 1, chloroplastic (EC 4.2.3.1) | protein | 430 | 42% helix, 16% strand | Q9S7B5 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 12 copies · chains A, B, C, D, E, F
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.83 | 0.84 | 108 | SAM |
| 2 | 849 | 0.82 | 0.84 | 108 | SAM |
| 3 | 769 | 0.79 | 0.83 | 95 | SAM |
| 4 | 1004 | 0.78 | 0.80 | 129 | PLP |
| 5 | 1053 | 0.78 | 0.80 | 122 | PLP |
Interfaces
6 interfaces between chains.
- E–F · 3645 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3630 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3589 Ų buried · 37 hydrogen bonds · protein-protein
- C–E · 356 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 269 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2C2B · Crystallographic structure of Arabidopsis thaliana Threonine synthase complexed with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9S7B5 · AlphaFold monomer V2.0 prediction for threonine synthase 1, chloroplastic (Q9S7B5) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 2C2B · PDBe 2C2B · UniProt Q9S7B5
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