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Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (ALPHAD60N) tryptophan synthase ALPHA2BETA2 complex reveals the correct orientation of active site alpha glu 49
Analyse Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A5A
- Type
- protein
- Length
- 644 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
- PLP, K
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase (alpha chain) (EC 4.2.1.20) | protein | 255 | 54% helix, 13% strand | P00929 |
| B | Tryptophan synthase (beta chain) (EC 4.2.1.20) | protein | 389 | 47% helix, 21% strand | P0A2K1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.79 | 0.85 | 95 | PLP |
| 2 | 536 | 0.70 | 0.79 | 52 | empty |
| 3 | 93 | 0.43 | 0.78 | 17 | empty |
| 4 | 72 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1356 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1A5A · Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant… · 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 0.98
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 1A5A · PDBe 1A5A · UniProt P00929 · UniProt P0A2K1
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