Research workbench
Crystal structure of salmonella typhimurium tryptophan synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2- methyl-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-L-serine at the beta-site
Analyse Crystal structure of salmonella typhimurium tryptophan synthase with sodium ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZ4
- Type
- protein
- Length
- 650 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
- KOU, NA, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 255 | 52% helix, 14% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 48% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- KOU · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 8 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 12 copies · chains A, B
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 | 129 | 0.79 | 0.97 | 37 | KOU |
| 2 | 301 | 0.65 | 0.80 | 37 | DMS |
| 3 | 101 | 0.46 | 0.80 | 26 | empty |
| 4 | 100 | 0.41 | 0.77 | 15 | DMS |
| 5 | 72 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6DZ4 · Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the… · 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 6DZ4 · PDBe 6DZ4 · UniProt P00929 · UniProt P0A2K1
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