1TCS

CRYSTAL STRUCTURE OF TRICHOSANTHIN-NADPH COMPLEX AT 1.7 ANGSTROMS RESOLUTION REVEALS ACTIVE-SITE ARCHITECTURE

• PDB DOI: https://doi.org/10.2210/pdb1TCS/pdb

• Classification: PROTEIN SYNTHESIS INHIBITOR
• Organism(s): Trichosanthes kirilowii
• Mutation(s): No 


• Deposited: 1994-12-27 Released: 1995-07-10 
• Deposition Author(s): Xiong, J.-P., Xia, Z.-X., Wang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of trichosanthin-NADPH complex at 1.7 A resolution reveals active-site architecture.

Xiong, J.P., Xia, Z.X., Wang, Y.

(1994) Nat Struct Biol 1: 695-700

• PubMed: 7634073 
• DOI: https://doi.org/10.1038/nsb1094-695
• Primary Citation of Related Structures:  
  1TCS


• PubMed Abstract: 
  

  We describe here the crystal structure of the trichosanthin-NADPH complex determined at a resolution of 1.7 A. The adenine base stacks between Tyr 70 and Tyr 111. Arg 163, Glu 160 and Tyr 70 form hydrogen bonds to N(3), O(3') and, through a water molecule, to N(9) of adenosine, respectively. This is the first high resolution structure of a complex between a ribosome-inactivating protein and a substrate analogue, in which the electron density of the N-glycosidic bond is well defined and the preassociated water, thought to be responsible for hydrolyzing the N-C bond, is also explicitly elucidated.

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Organizational Affiliation: 

Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.91 kDa 
• Atom Count: 2,107 
• Modelled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRICHOSANTHIN	A	247	Trichosanthes kirilowii	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P09989 (Trichosanthes kirilowii) Explore P09989  Go to UniProtKB:  P09989

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.39	α = 90
b = 76.81	β = 90
c = 79.93	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-07-10 
Deposition Author(s): Xiong, J.-P., Xia, Z.-X., Wang, Y.

Revision History  

• Version 1.0: 1995-07-10
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations