Research workbench
Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1- ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site
Analyse Crystal structure of mutant beta-K167T tryptophan synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DUC
- Type
- protein
- Length
- 660 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
- A0A0D6FWC1, A0A0J0ZFZ1
- Ligands
- F9F, 1D0, 2AP, CS, CL
- Pockets
- 5 · best druggability 0.80
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 | 265 | 50% helix, 15% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 47% helix, 22% strand | A0A0J0ZFZ1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · chains A, B
- 1D0 · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid · ligand · chains B
- 2AP · 2-aminopyridine · ligand · chains B
- CS · Cesium ion · metal · 3 copies · chains B
- CL · Chloride ion · ion · 11 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.97 | 36 | F9F |
| 2 | 123 | 0.80 | 0.98 | 36 | 1D0 |
| 3 | 134 | 0.50 | 0.80 | 26 | empty |
| 4 | 56 | 0.37 | 0.79 | 14 | empty |
| 5 | 67 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1379 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6DUC · Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor… · 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 A0A0D6FWC1
- Every structure of UniProt A0A0J0ZFZ1
- Elsewhere: RCSB PDB 6DUC · PDBe 6DUC · UniProt A0A0D6FWC1 · UniProt A0A0J0ZFZ1
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