3N3X

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution

Kushwaha, G.S.Vikram, G.Sinha, M.Kaur, P.Sharma, S.Singh, T.P.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome inactivating protein246Momordica balsaminaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for D9J2T9 (Momordica balsamina)
Explore D9J2T9 
Go to UniProtKB:  D9J2T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9J2T9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SDDDMG peptide6N/AMutation(s): 0 
UniProt
Find proteins for P02400 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02400 
Go to UniProtKB:  P02400
Entity Groups  
UniProt GroupP02400
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GUN
Query on GUN

Download Ideal Coordinates CCD File 
D [auth A]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.210 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.241α = 90
b = 130.241β = 90
c = 39.974γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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