Research workbench
Crystal structure of wild-type tryptophan synthase complexed with 1- [(2-HYDROXYLPHENYL)AMINO]3-glycerolphosphate
Analyse Crystal structure of wild-type tryptophan synthase complexed with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TJP
- Type
- protein
- Length
- 661 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, P00933
- Ligands
- HPF, PLP, NA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 267 | 49% helix, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 394 | 48% helix, 21% strand | P00933 |
Ligands and binding sites
- HPF · 1-[(2-hydroxylphenyl)amino]3-glycerolphosphate · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.80 | 0.98 | 35 | HPF |
| 2 | 174 | 0.76 | 0.92 | 39 | PLP |
| 3 | 138 | 0.50 | 0.80 | 30 | empty |
| 4 | 92 | 0.43 | 0.78 | 18 | empty |
| 5 | 64 | 0.36 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1429 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1TJP · Crystal Structure Of Wild-Type Tryptophan Synthase Complexed With… · the same entry in another collection · chain B against B, 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 P00933
- Elsewhere: RCSB PDB 1TJP · PDBe 1TJP · UniProt P00929 · UniProt P00933
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