3MY6 | pdb_00003my6

Crystal Structure of the complex of type 1 ribosome inactivating protein with 7-methylguanine at 2.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3MY6/pdb

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


• Deposited: 2010-05-10 Released: 2010-08-04 
• Deposition Author(s): Kushwaha, G.S., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.210 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the complex of type 1 ribosome inactivating protein with 7-methylguanine at 2.65 A resolution

Kushwaha, G.S., Singh, N., Sinha, M., Bhushan, A., 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: 27.66 kDa 
• Atom Count: 2,063 
• Modeled 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 momordin I	A	246	Momordica balsamina	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for E0CX04 (Momordica balsamina) Explore E0CX04  Go to UniProtKB:  E0CX04
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MY6	C [auth A]	2-amino-7-methyl-1,7-dihydro-6H-purin-6-one C6 H7 N5 O FZWGECJQACGGTI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.210 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.428	α = 90
b = 131.428	β = 90
c = 39.808	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Kushwaha, G.S., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary