MolNFT v1 · #181445 · protein
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 L-histidine at the enzyme beta-site at 1.55 ångström resolution
7LV5 · Tryptophan synthase alpha chain: “The internal aldimine form of the wild-type salmonella typhimurium tryptophan synthase in complex with…”. X-ray diffraction, 6 ligands (F9F, PLP, BCN), 6 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 7LV5
- 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, BCN, HIS, CS, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% 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, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 393 | 47% helix, 21% 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
- BCN · Bicine · ligand · chains B
- HIS · Histidine · ligand · chains B
- CS · Cesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
- GOL · Glycerol · additive · chains A
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 | 142 | 0.81 | 0.97 | 39 | F9F |
| 2 | 310 | 0.75 | 0.87 | 57 | PLP, HIS |
| 3 | 86 | 0.38 | 0.77 | 14 | DMS |
| 4 | 97 | 0.37 | 0.75 | 20 | empty |
| 5 | 61 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1447 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7LV5 · The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in… · the same entry in another collection · chain B against B, 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
- P00929 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P00929) · a predicted model of the same protein · chain A 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 P00929
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 7LV5 · PDBe 7LV5 · UniProt P00929 · UniProt P0A2K1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.