1TFM

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

Mishra, V.Bilgrami, S.Paramasivam, M.Yadav, S.Sharma, R.S.Kaur, P.Srinivasan, A.Babu, C.R.Singh, T.P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Himalayan mistletoe ribosome-inactivating protein A240Viscum albumMutation(s): 0 
EC: 3.2.2.22
Find proteins for Q6ITZ3 (Viscum album)
Explore Q6ITZ3 
Go to UniProtKB:  Q6ITZ3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Himalayan mistletoe ribosome-inactivating protein B255Viscum albumMutation(s): 0 
EC: 3.2.2.22
Find proteins for Q6ITZ3 (Viscum album)
Explore Q6ITZ3 
Go to UniProtKB:  Q6ITZ3
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
F
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6C
Query on P6C

Download Ideal Coordinates CCD File 
A
2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID
C10 H11 N5 O2
GPHPGFBRJYCUDO-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GAL
Query on GAL

Download Ideal Coordinates CCD File 
B
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004
Fbeta-lactoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.240 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.422α = 90
b = 109.422β = 90
c = 309.798γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary