MolNFT v1 · #179824 · protein
1.45 ångström resolution internal aldimine crystal structure of the beta-Q114A mutant of tryptophansynthase in complex with N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site
7KH6 · Tryptophan synthase alpha chain: “1.45 ångström resolution internal aldimine crystal structure of the beta-Q114A mutant of tryptophansynthase…”. X-ray diffraction, 4 ligands (F9F, PLP, CS), 7 pockets (best druggability 0.81). MolNFT…
- PDB
- 7KH6
- Type
- protein
- Length
- 662 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
- F9F, PLP, CS, CL
- Pockets
- 7 · 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 alpha chain (EC 4.2.1.20) | protein | 268 | 50% helix, 13% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 394 | 47% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- CS · Cesium ion · metal · 3 copies · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.81 | 0.97 | 34 | F9F |
| 2 | 424 | 0.76 | 0.85 | 67 | PLP |
| 3 | 83 | 0.37 | 0.76 | 15 | DMS |
| 4 | 69 | 0.37 | 0.78 | 20 | empty |
| 5 | 85 | 0.35 | 0.75 | 18 | DMS |
Interfaces
1 interface between chains.
- A–B · 1443 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7KH6 · 1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of… · the same entry in another collection · chain A against A, TM-score 1.00
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 7KH6 · PDBe 7KH6 · UniProt P00929 · UniProt P0A2K1
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