3N1D

Crystal structure of the complex of type I ribosome inactivating protein with ribose at 1.7A resolution

• PDB DOI: https://doi.org/10.2210/pdb3N1D/pdb

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


• Deposited: 2010-05-15 Released: 2010-06-23 
• 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: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Crystal structure of the complex of type I ribosome inactivating protein with ribose at 1.7A resolution

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

To be published.

Biological Assembly 1  

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: 2,204 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome inactivating protein	A	246	Momordica balsamina	Mutation(s): 0  EC: 3.2.2.22
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIP	C [auth A]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.968	α = 90
b = 129.968	β = 90
c = 40.244	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

• Released Date: 2010-06-23 
Deposition Author(s): Pandey, N., Kushwaha, G.S., Sinha, M., Kaur, P., Betzel, C., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-06-23
  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
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary