Research workbench
TRP synthase (D60N-ipp-ser) with K+
Analyse TRP synthase (D60N-ipp-ser) with K+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BEU
- Type
- protein
- Length
- 642 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
- IPL, PLS, K
- Pockets
- 5 · best druggability 0.76
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 | 253 | 54% helix, 13% strand | P00929 |
| B | Tryptophan synthase (EC 4.2.1.20) | protein | 389 | 48% helix, 21% strand | P0A2K1 |
Ligands and binding sites
- IPL · Indole-3-propanol phosphate · ligand · chains A
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · chains B
- K · Potassium 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 | 380 | 0.76 | 0.86 | 72 | PLS |
| 2 | 375 | 0.67 | 0.80 | 34 | IPL |
| 3 | 79 | 0.38 | 0.77 | 15 | empty |
| 4 | 71 | 0.37 | 0.78 | 19 | empty |
| 5 | 62 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1367 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1BEU · TRP synthase (D60N-ipp-ser) with K+ · 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 1BEU · PDBe 1BEU · UniProt P00929 · UniProt P0A2K1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.