MolNFT v1 · #180142 · protein
The internal aldimine form of the wild-type tryptophan synthase from salmonella in complex with inhibitor N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.47 ångström resolution
7KQF · Tryptophan synthase alpha chain: “The internal aldimine form of the wild-type tryptophan synthase from salmonella in complex with inhibitor…”. X-ray diffraction, 4 ligands (F9F, PLP, CS), 5 pockets (best druggability 0.80). MolNFT…
- PDB
- 7KQF
- 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, CS, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 268 | 49% helix, 13% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 393 | 49% 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
- CS · Cesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.80 | 0.97 | 35 | F9F |
| 2 | 325 | 0.75 | 0.87 | 62 | PLP, EDO |
| 3 | 95 | 0.36 | 0.75 | 19 | empty |
| 4 | 75 | 0.33 | 0.75 | 19 | empty |
| 5 | 59 | 0.25 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1432 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7KQF · The internal aldimine form of the wild-type Tryptophan Synthase from Salmonella in… · 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 7KQF · PDBe 7KQF · UniProt P00929 · UniProt P0A2K1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.