MolNFT v1 · #56849 · protein
Crystal structure of threonine synthase from aquifex aeolicus VF5
2ZSJ: “Crystal structure of threonine synthase from aquifex aeolicus VF5”. X-ray diffraction, 1 ligand (PLP), 14 pockets (best druggability 0.76). MolNFT v1 #56849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZSJ
- Type
- protein
- Length
- 1,398 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- O66740
- Ligands
- PLP
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Threonine synthase (EC 4.2.3.1) | protein | 350 | 47% helix, 17% strand | O66740 |
| D | Threonine synthase (EC 4.2.3.1) | protein | 348 | 46% helix, 17% strand | O66740 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.76 | 0.81 | 68 | PLP |
| 2 | 692 | 0.75 | 0.81 | 76 | PLP |
| 3 | 629 | 0.75 | 0.81 | 75 | PLP |
| 4 | 582 | 0.73 | 0.81 | 70 | PLP |
| 5 | 217 | 0.72 | 0.88 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3238 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3235 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2ZSJ · Crystal structure of threonine synthase from Aquifex aeolicus VF5 · 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 O66740
- Elsewhere: RCSB PDB 2ZSJ · PDBe 2ZSJ · UniProt O66740
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.