Research workbench
The internal aldimine form of the wild-type salmonella typhimurium tryptophan synthase in complex with inhibitor N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 ångström resolution. one of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the plp oxygen at the position 3 in the ring
Analyse The internal aldimine form of the wild-type salmonella typhimurium tryptophan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LKL
- 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
- A0A0D6FWC1, P0A2K1
- Ligands
- TRP, F9F, PLP, CS, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 268 | 49% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 393 | 46% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- CS · Cesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.97 | 30 | F9F |
| 2 | 150 | 0.80 | 0.96 | 36 | TRP, PLP |
| 3 | 237 | 0.58 | 0.79 | 49 | DMS, CL |
| 4 | 92 | 0.38 | 0.76 | 14 | empty |
| 5 | 59 | 0.37 | 0.79 | 13 | CL |
Interfaces
1 interface between chains.
- A–B · 1461 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7LKL · The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A2K1 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain (P0A2K1) · a predicted model of the same protein · chain B 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 A0A0D6FWC1
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 7LKL · PDBe 7LKL · UniProt A0A0D6FWC1 · UniProt P0A2K1
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