3Q4P

Crystal structure of the complex of type I ribosome inactivating protein with 7n-methyl -8-hydroguanosine-5-p-diphosphate at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3Q4P/pdb

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


• Deposited: 2010-12-24 Released: 2011-01-12 
• Deposition Author(s): Kushwaha, G.S., Yamini, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Crystal structure of the complex of type I ribosome inactivating protein with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.8 A resolution

Kushwaha, G.S., Yamini, S., Sinha, M., Kaur, P., 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: 27.97 kDa 
• Atom Count: 2,147 
• 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
UniProt
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9  Go to UniProtKB:  D9J2T9
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7G	B [auth A]	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE C11 H18 N5 O11 P2 SBASPRRECYVBRF-KQYNXXCUSA-O
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	C [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: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.848	α = 90
b = 129.848	β = 90
c = 39.717	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: 2011-01-12 
Deposition Author(s): Kushwaha, G.S., Yamini, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.0: 2024-11-20
  Changes: Data collection, Non-polymer description, Structure summary