Research workbench
Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site
Analyse Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PR2
- Type
- protein
- Length
- 657 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
- F9F, 7MN, CS
- Pockets
- 7 · best druggability 0.84
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 | 266 | 50% helix, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 391 | 47% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- 7MN · (Z)-N-[(1E)-1-carboxy-2-(2,3-dihydro-1H-indol-1-yl)ethylidene]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methanaminium · ligand · chains B
- CS · Cesium ion · metal · 3 copies · chains 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 | 204 | 0.84 | 0.97 | 49 | 7MN |
| 2 | 140 | 0.80 | 0.97 | 37 | F9F |
| 3 | 123 | 0.45 | 0.77 | 21 | empty |
| 4 | 80 | 0.44 | 0.80 | 18 | empty |
| 5 | 79 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1379 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3PR2 · Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site · 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 1.00
- 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 3PR2 · PDBe 3PR2 · UniProt P00929 · UniProt P0A2K1
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