1TCS

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 molecul ...

    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.


    Related Citations: 
    • The Three-Dimensional Structure of Trichosanthin Refined at 2.7 Angstroms Resolution
      Xia, Z.-X., Zhang, L., Zhang, Z.-M.
      (1993) Chin J Chem 11: 280
    • The Revision of Three-Dimensional Structure of Trichosanthin at 3 Angstroms Resolution
      Xia, Z.-X., Zhang, Z.-M., Zhang, L.
      (1991) Chin J Chem 9: 563

    Organizational Affiliation

    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRICHOSANTHIN A247Trichosanthes kirilowiiMutation(s): 0 
EC: 3.2.2.22
Find proteins for P09989 (Trichosanthes kirilowii)
Explore P09989 
Go to UniProtKB:  P09989
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.39α = 90
b = 76.81β = 90
c = 79.93γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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