Research workbench
Crystal structure of tryptophan synthase from salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site
Analyse Crystal structure of tryptophan synthase from salmonella typhimurium in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WX2
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain
- EC
- 4.2.1.20
- UniProt
- P00929, P0A2K1
- Ligands
- F6F, PLP, NA
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 253 | 52% helix, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 49% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- F6F · 2-{[4-(trifluoromethoxy)benzoyl]amino}ethyl dihydrogen phosphate · ligand · 3 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.80 | 0.89 | 71 | PLP, F6F |
| 2 | 276 | 0.69 | 0.84 | 39 | F6F |
| 3 | 91 | 0.36 | 0.75 | 22 | empty |
| 4 | 53 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4WX2 · Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two… · 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 P00929
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 4WX2 · PDBe 4WX2 · UniProt P00929 · UniProt P0A2K1
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