3N2D

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution

Kushwaha, G.S.Prem Kumar, R.Sinha, M.Bhushan, A.Kaur, P.Sharma, S.Singh, T.P.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome inactivating proteinA246Momordica balsaminaMutation(s): 0 
Gene Names: RIP
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
6-meric peptide from 60S acidic ribosomal protein P2-betaB6Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02400 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02400 
Go to UniProtKB:  P02400
Entity Groups  
UniProt GroupP02400
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.186α = 90
b = 131.186β = 90
c = 40.734γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    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