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The crystal structure of tryptophan synthase from salmonella enterica serovar typhimurium in complex with (2S)-3-amino-3-imino-2- phenyldiazenylpropanamide at the enzyme alpha-site.
Analyse The crystal structure of tryptophan synthase from salmonella enterica serovar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XIN
- Type
- protein
- Length
- 654 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
- PLP, V41, CS, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 258 | 52% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 47% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- V41 · (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide · ligand · chains A, B
- CS · Cesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 14 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 24 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 648 | 0.78 | 0.84 | 68 | PLP, CL, EDO |
| 2 | 435 | 0.76 | 0.84 | 51 | CL, DMS, V41 |
| 3 | 66 | 0.44 | 0.82 | 17 | empty |
| 4 | 97 | 0.42 | 0.77 | 14 | DMS |
| 5 | 69 | 0.33 | 0.75 | 17 | DMS |
Interfaces
1 interface between chains.
- A–B · 1435 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6XIN · The crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium… · 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 6XIN · PDBe 6XIN · UniProt A0A0D6FWC1 · UniProt P0A2K1
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