Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.40 kDa 
• Atom Count: 2058 
• Residue Count: 246 
• Unique protein chains: 1

1MRG

STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS

• DOI: 10.2210/pdb1MRG/pdb

• Classification: RIBOSOME-INACTIVATING PROTEIN
• Organism(s): Momordica charantia
• Mutation(s): No 


• Deposited: 1994-07-01 Released: 1995-02-07 
• Deposition Author(s): Huang, Q., Liu, S., Tang, Y., Jin, S., Wang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins.

Huang, Q., Liu, S., Tang, Y., Jin, S., Wang, Y.

(1995) Biochem J 309: 285-298

• PubMed: 7619070 
• Primary Citation of Related Structures:  
  1MRK, 1MRJ, 1MRI, 1MRH, 1MRG


• PubMed Abstract: 
  

Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre.

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Related Citations: 

• Active Center Geometry and Depurine Mechanism of Two Ribosome-Inactivating Proteins
  Tang, Y., Huang, Q.
  (1994) Prog Nat Sci 4: 527

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Organizational Affiliation: 

Department of Chemistry, Peking University, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-MOMORCHARIN	A	263	Momordica charantia	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P16094 (Momordica charantia) Explore P16094  Go to UniProtKB:  P16094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	A	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.6	α = 90
b = 131.6	β = 90
c = 39.7	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-01 
• Released Date: 1995-02-07 
Deposition Author(s): Huang, Q., Liu, S., Tang, Y., Jin, S., Wang, Y.

Revision History 

• Version 1.0: 1995-02-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance