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Crystal structure of tryptophan synthase from salmonella typhimurium in complex with 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL dihydrogen phosphate (F9F) inhibitor in the alpha site and ammonium ion in the metal coordination 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
- 4XUG
- Type
- protein
- Length
- 661 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
- F9F, PLP, NH4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 267 | 49% helix, 13% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 394 | 47% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- NH4 · Ammonium ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.97 | 34 | F9F |
| 2 | 313 | 0.74 | 0.86 | 61 | PLP, EDO |
| 3 | 77 | 0.37 | 0.77 | 14 | empty |
| 4 | 94 | 0.37 | 0.75 | 24 | empty |
| 5 | 65 | 0.35 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1442 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4XUG · Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with… · 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 4XUG · PDBe 4XUG · UniProt P00929 · UniProt P0A2K1
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