MolNFT v1 · #169935 · protein
Salmonella typhimurium tryptophan synthase complexed with oxindolyl-L- alanine and D-glycerol-3-phosphate
6XRH · Tryptophan synthase alpha chain: “Salmonella typhimurium tryptophan synthase complexed with oxindolyl-L- alanine and D-glycerol-3-phosphate”. X-ray diffraction, 4 ligands (1GP, VCP, VCS), 6 pockets (best druggability 0.83). MolNFT…
- PDB
- 6XRH
- 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, VCP, VCS, NA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 267 | 50% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 396 | 46% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · chains A
- VCP · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine · ligand · chains B
- VCS · 4-[(E)-({1-carboxy-2-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate · ligand · chains B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.83 | 0.97 | 45 | VCP, VCS |
| 2 | 157 | 0.81 | 0.97 | 40 | 1GP |
| 3 | 106 | 0.42 | 0.77 | 26 | empty |
| 4 | 83 | 0.41 | 0.78 | 16 | DMS |
| 5 | 96 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1429 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6XRH · Salmonella typhimurium tryptophan synthase complexed with oxindolyl-L-alanine and… · 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 6XRH · PDBe 6XRH · UniProt A0A0D6FWC1 · UniProt P0A2K1
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