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Salmonella typhimurium tryptophan synthase complexed with dioxindolyl- L-alanine and D-glycerol-3-phosphate
Analyse Salmonella typhimurium tryptophan synthase complexed with dioxindolyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XT0
- Type
- protein
- Length
- 663 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
- 1GP, X9D, VE4, NA
- 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 | 267 | 50% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 46% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · chains A
- X9D · 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate · ligand · chains B
- VE4 · 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate · ligand · chains B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 15 copies · chains A, B
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 | 150 | 0.81 | 0.97 | 39 | 1GP |
| 2 | 154 | 0.81 | 0.97 | 35 | X9D, VE4 |
| 3 | 109 | 0.45 | 0.79 | 21 | empty |
| 4 | 88 | 0.41 | 0.77 | 15 | DMS |
| 5 | 77 | 0.34 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1434 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6XT0 · Salmonella typhimurium tryptophan synthase complexed with dioxindolyl-L-alanine and… · 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 6XT0 · PDBe 6XT0 · UniProt A0A0D6FWC1 · UniProt P0A2K1
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