MolNFT v1 · #2839 · protein
Crystal structure of the complex of bacterial tryptophan synthase with the transition state analogue inhibitor 4-(2-hydroxyphenylthio)- butylphosphonic acid
1C8V: “Crystal structure of the complex of bacterial tryptophan synthase with the transition state analogue…”. X-ray diffraction, 3 ligands (HE1, PLP, NA), 8 pockets (best druggability 0.81). MolNFT v1 #2839 on GenesisL1: 3D structure…
- PDB
- 1C8V
- Type
- protein
- Length
- 651 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
- HE1, PLP, NA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase (EC 4.2.1.20) | protein | 264 | 50% helix, 14% strand | P00929 |
| B | Tryptophan synthase (EC 4.2.1.20) | protein | 387 | 46% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- HE1 · 4-(2-hydroxyphenylthio)-1-butenylphosphonic 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
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 | 149 | 0.81 | 0.96 | 34 | HE1 |
| 2 | 377 | 0.76 | 0.86 | 60 | PLP |
| 3 | 53 | 0.70 | 0.98 | 19 | empty |
| 4 | 88 | 0.42 | 0.79 | 23 | empty |
| 5 | 95 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1411 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1C8V · Crystal structure of the complex of bacterial tryptophan synthase with the transition… · the same entry in another collection · chain A against A, 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 1C8V · PDBe 1C8V · UniProt P00929 · UniProt P0A2K1
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