MolNFT v1 · #179583 · protein
1.60 ångström resolution crystal structure of the beta-Q114A mutant tryptophan synthase in complex with inhibitor N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site
7KA1 · Tryptophan synthase alpha chain: “1.60 ångström resolution crystal structure of the beta-Q114A mutant tryptophan synthase in complex with…”. X-ray diffraction, 5 ligands (F9F, 0JO, SER), 7 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7KA1
- Type
- protein
- Length
- 663 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, 0JO, SER, CS, CL
- Pockets
- 7 · 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 | 268 | 50% helix, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 47% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · chains B
- SER · Serine · ligand · chains A, B
- CS · Cesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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 | 125 | 0.79 | 0.97 | 32 | F9F |
| 2 | 139 | 0.78 | 0.96 | 43 | 0JO |
| 3 | 115 | 0.44 | 0.77 | 23 | DMS, SER |
| 4 | 90 | 0.40 | 0.77 | 18 | empty |
| 5 | 83 | 0.39 | 0.77 | 14 | DMS |
Interfaces
1 interface between chains.
- A–B · 1408 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7KA1 · 1.60 Angstrom resolution crystal structure of the beta-Q114A mutant Tryptophan Synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A2K1 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain (P0A2K1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 7KA1 · PDBe 7KA1 · UniProt P00929 · UniProt P0A2K1
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