Research workbench
The external aldimine form of the mutant beta-S377A salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-site. 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 external aldimine form of the mutant beta-S377A salmonella thypi tryptophan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JMQ
- Type
- protein
- Length
- 664 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, KOU, CS, NA, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% 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, 14% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 46% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- KOU · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine · ligand · chains B
- CS · Cesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 33 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.83 | 0.98 | 47 | DMS, F9F |
| 2 | 141 | 0.80 | 0.97 | 36 | KOU, GOL |
| 3 | 145 | 0.49 | 0.79 | 31 | DMS |
| 4 | 93 | 0.40 | 0.77 | 14 | DMS |
| 5 | 77 | 0.39 | 0.78 | 17 | DMS |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7JMQ · The external aldimine form of the mutant beta-S377A Salmonella thypi tryptophan synthase… · 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
- 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 7JMQ · PDBe 7JMQ · UniProt P00929 · UniProt P0A2K1
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