MolNFT v1 · #50972 · protein
Crystal structures of mutant (BETAK87T) tryptophan synthase ALPHA2 BETA2 complex with ligands bound to the active sites of the alpha and beta subunits reveal ligand-induced conformational changes
2TYS: “Crystal structures of mutant (BETAK87T) tryptophan synthase ALPHA2 BETA2 complex with ligands bound to the…”. X-ray diffraction, 2 ligands (PLT, NA), 5 pockets (best druggability 0.82). MolNFT v1 #50972 on GenesisL1: 3D structure…
- PDB
- 2TYS
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase
- EC
- 4.2.1.20
- UniProt
- P00929, P0A2K1
- Ligands
- PLT, NA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase (EC 4.2.1.20) | protein | 255 | 55% helix, 14% strand | P00929 |
| B | Tryptophan synthase (EC 4.2.1.20) | protein | 395 | 47% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- PLT · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-L-tryptophane · ligand · chains B
- NA · Sodium ion · metal · 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 | 164 | 0.82 | 0.97 | 33 | PLT |
| 2 | 372 | 0.67 | 0.80 | 42 | empty |
| 3 | 75 | 0.42 | 0.79 | 15 | empty |
| 4 | 108 | 0.41 | 0.77 | 20 | empty |
| 5 | 95 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1286 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2TYS · Crystal structures of mutant (BETAK87T) tryptophan synthase ALPHA2 BETA2 complex with… · the same entry in another collection · chain B against B, 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 2TYS · PDBe 2TYS · UniProt P00929 · UniProt P0A2K1
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