Research workbench
The internal aldimine form of salmonella typhimurium tryptophan synthase mutant beta-Q114A with cesium ion at the metal coordination site. a random beta-P270L mutation was inserted during PCR step
Analyse The internal aldimine form of salmonella typhimurium tryptophan synthase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0B
- Type
- protein
- Length
- 651 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
- SER, PLP, BCN, CS, CL
- Pockets
- 5 · best druggability 0.80
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, 14% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 47% helix, 20% strand | P0A2K1 |
Ligands and binding sites
- SER · Serine · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- BCN · Bicine · ligand · chains B
- CS · Cesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 17 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains B
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 | 455 | 0.80 | 0.88 | 75 | PLP, EDO, BCN |
| 2 | 289 | 0.64 | 0.80 | 36 | DMS |
| 3 | 93 | 0.39 | 0.76 | 15 | DMS |
| 4 | 70 | 0.36 | 0.77 | 20 | empty |
| 5 | 50 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0B · The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant… · 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
- P00929 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P00929) · a predicted model of the same protein · chain A 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 P00929
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 7K0B · PDBe 7K0B · UniProt P00929 · UniProt P0A2K1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.