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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).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATryptophan synthase alpha chain (EC 4.2.1.20)protein26550% helix, 15% strandA0A0D6FWC1
BTryptophan synthase beta chain (EC 4.2.1.20)protein39547% helix, 22% strandA0A0J0ZFZ1

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11390.800.9736F9F
21230.800.98361D0
31340.500.8026empty
4560.370.7914empty
5670.320.7515empty

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

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