MolNFT v1 · #168983 · protein
High resolution tryptophan synthase crystal structure from salmonella typhimurium in complex with F9 inhibitor in the alpha-site, cesium ion at the metal coordination site and internal aldimine form.
6WX3 · Tryptophan synthase alpha chain: “High resolution tryptophan synthase crystal structure from salmonella typhimurium in complex with F9…”. X-ray diffraction, 5 ligands (BCN, F9F, PLP), 7 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6WX3
- Type
- protein
- Length
- 657 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
- BCN, F9F, PLP, CS, CL
- Pockets
- 7 · 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, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 389 | 48% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- BCN · Bicine · ligand · 4 copies · chains B, A
- 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 · 2 copies · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.81 | 0.97 | 36 | F9F |
| 2 | 320 | 0.74 | 0.86 | 58 | PLP |
| 3 | 54 | 0.35 | 0.79 | 17 | empty |
| 4 | 66 | 0.32 | 0.75 | 14 | empty |
| 5 | 68 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1445 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6WX3 · High resolution Tryptophan Synthase crystal structure from Salmonella typhimurium 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 A0A0D6FWC1
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 6WX3 · PDBe 6WX3 · UniProt A0A0D6FWC1 · UniProt P0A2K1
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