5JM1

Structure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal beta-(1,4) Gal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agglutinin alpha chain
A, C, E, G
133Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18670 (Artocarpus integer)
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Go to UniProtKB:  P18670
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18670
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Agglutinin beta-3 chain
B, D, F, H
19Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18673 (Artocarpus integer)
Explore P18673 
Go to UniProtKB:  P18673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18673
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose
I
3N/A
Glycosylation Resources
GlyTouCan:  G31408VE
GlyCosmos:  G31408VE
GlyGen:  G31408VE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMG
Query on AMG

Download Ideal Coordinates CCD File 
U [auth G]methyl alpha-D-galactopyranoside
C7 H14 O6
HOVAGTYPODGVJG-PZRMXXKTSA-N
PEG
Query on PEG

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N [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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J [auth A]
K [auth A]
L [auth A]
M [auth C]
O [auth D]
J [auth A],
K [auth A],
L [auth A],
M [auth C],
O [auth D],
P [auth E],
Q [auth G],
R [auth G],
S [auth G],
T [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.49α = 90
b = 81.58β = 107.65
c = 63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science and Technology, Govt. of IndiaIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary