MolNFT v1 · #2857 · protein
Crystal structure of the complex of bacterial tryptophan synthase with the transition state analogue inhibitor 4-(2-hydroxy-4- fluorophenylthio)-butylphosphonic acid
1C9D · Tryptophan synthase (alpha chain): “Crystal structure of the complex of bacterial tryptophan synthase with the transition state analogue…”. X-ray diffraction, 3 ligands (HF1, PLP, NA), 9 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 1C9D
- Type
- protein
- Length
- 651 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
- HF1, PLP, NA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase (alpha chain) (EC 4.2.1.20) | protein | 264 | 50% helix, 14% strand | P00929 |
| B | Tryptophan synthase (beta chain) (EC 4.2.1.20) | protein | 387 | 46% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- HF1 · 4-(2-hydroxy-4-fluorophenylthio)-butylphosphonic acid · 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.79 | 0.96 | 34 | HF1 |
| 2 | 250 | 0.77 | 0.90 | 42 | PLP |
| 3 | 102 | 0.43 | 0.78 | 20 | empty |
| 4 | 67 | 0.42 | 0.80 | 18 | empty |
| 5 | 87 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1C9D · Crystal structure of the complex of bacterial tryptophan synthase with the transition… · 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 P0A2K1
- Elsewhere: RCSB PDB 1C9D · PDBe 1C9D · UniProt P00929 · UniProt P0A2K1
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