Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.79 kDa 
• Atom Count: 2103 
• Residue Count: 246 
• Unique protein chains: 1

3N5D

Crystal structure of the complex of type I ribosome inactivating protein with glucose at 1.9A resolution

• DOI: 10.2210/pdb3N5D/pdb

• Classification: HYDROLASE
• Organism(s): Momordica balsamina
• Mutation(s): No 


• Deposited: 2010-05-25 Released: 2010-06-30 
• Deposition Author(s): Pandey, N., Kushwaha, G.S., Sinha, M., Kaur, P., Betzel, C., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.250 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Crystal structure of the complex of type I ribosome inactivating protein with glucose at 1.9A resolution

Pandey, N., Kushwaha, G.S., Sinha, M., Kaur, P., Betzel, C., Sharma, S., Singh, T.P.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome inactivating protein	A	246	Momordica balsamina	Mutation(s): 0  Gene Names: RIP EC: 3.2.2.22
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9  Go to UniProtKB:  D9J2T9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	A	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.250 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.666	α = 90
b = 130.666	β = 90
c = 40.498	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-25 
• Released Date: 2010-06-30 
Deposition Author(s): Pandey, N., Kushwaha, G.S., Sinha, M., Kaur, P., Betzel, C., Sharma, S., Singh, T.P.

Revision History 

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary