Research workbench
Salmonella typhimurium tryptophan synthase complexed with L-tryptophan and D-glycerol-3-phosphate
Analyse Salmonella typhimurium tryptophan synthase complexed with L-tryptophan and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XNC
- 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, PLP, TRP, NA
- Pockets
- 10 · 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 | 49% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 46% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- TRP · Tryptophan · ligand · chains B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 28 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.81 | 0.97 | 42 | DMS, 1GP |
| 2 | 129 | 0.79 | 0.97 | 36 | PLP, TRP |
| 3 | 136 | 0.50 | 0.79 | 31 | DMS |
| 4 | 74 | 0.47 | 0.82 | 18 | empty |
| 5 | 80 | 0.43 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1451 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (pyridoxal phosphate Schiff base, additive adduct).
Compared structures
- 6XNC · Salmonella typhimurium tryptophan synthase complexed with L-tryptophan and… · 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
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 6XNC · PDBe 6XNC · UniProt A0A0D6FWC1 · UniProt P0A2K1
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