Research workbench
The internal aldimine form of the wild-type salmonella typhimurium tryptophan synthase with cesium ion at the metal coordination site at 1.60 ångström resolution
Analyse The internal aldimine form of the wild-type salmonella typhimurium tryptophan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4D
- Type
- protein
- Length
- 652 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
- PLP, CS, CL
- Pockets
- 7 · best druggability 0.76
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 | 256 | 52% helix, 13% strand | P00929 |
| 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
- CS · Cesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 25 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- GOL · Glycerol · additive · chains A
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 | 193 | 0.76 | 0.91 | 46 | PLP, DMS, CL |
| 2 | 306 | 0.64 | 0.80 | 37 | DMS |
| 3 | 71 | 0.47 | 0.83 | 18 | PEG |
| 4 | 85 | 0.41 | 0.79 | 18 | empty |
| 5 | 98 | 0.39 | 0.76 | 14 | DMS |
Interfaces
1 interface between chains.
- A–B · 1335 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7L4D · The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase… · 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 P00929
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 7L4D · PDBe 7L4D · UniProt P00929 · UniProt P0A2K1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.