Research workbench
The internal aldimine form of the wild-type salmonella typhimurium tryptophan synthase in complex with N-(4'-trifluoromethoxybenzoyl)-2- amino-1-ethylphosphate (F6F) inhibitor at the alpha-and beta-site, sodium ion at the metal coordination site, and another F6F molecule at the enzyme beta-site at 1.55 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
- 7M3S
- 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
- F6F, PLP, NA, CL
- Pockets
- 5 · 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 | 265 | 50% helix, 14% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 47% helix, 20% strand | P0A2K1 |
Ligands and binding sites
- F6F · 2-{[4-(trifluoromethoxy)benzoyl]amino}ethyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- DMS · Dimethyl sulfoxide · additive · chains B
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 | 194 | 0.81 | 0.96 | 46 | PLP, F6F |
| 2 | 131 | 0.80 | 0.97 | 35 | F6F |
| 3 | 99 | 0.44 | 0.79 | 27 | empty |
| 4 | 74 | 0.38 | 0.78 | 21 | empty |
| 5 | 70 | 0.37 | 0.77 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 1444 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7M3S · 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
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 7M3S · PDBe 7M3S · UniProt P00929 · UniProt P0A2K1
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