4AKC

Structure of Galactose Binding lectin from Champedak (CGB) with Gal(beta)1,3-GalNac

• PDB DOI: https://doi.org/10.2210/pdb4AKC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Artocarpus integer
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2013-02-27 
• Deposition Author(s): Gabrielsen, M., Abdul-Rahman, P.S., Othman, S., Hashim, O.H., Cogdell, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins from Champedak: Differences from Jackfruit Lectins

Gabrielsen, M., Abdul-Rahman, P.S., Othman, S., Hashim, O.H., Cogdell, R.J.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 709

• PubMed: 24915077 
• DOI: https://doi.org/10.1107/S2053230X14008966
• Primary Citation of Related Structures:  
  4AK4, 4AKB, 4AKC, 4AKD


• PubMed Abstract: 
  

  Galactose-binding and mannose-binding lectins from the champedak fruit, which is native to South-east Asia, exhibit useful potential clinical applications. The specificity of the two lectins for their respective ligands allows the detection of potential cancer biomarkers and monitoring of the glycosylated state of proteins in human serum and/or urine. To fully understand and expand the use of these natural proteins, their complete sequences and crystal structures are presented here, together with details of sugar binding.

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Organizational Affiliation: 

Institute of Molecular, Cell and Systems Biology, University of Glasgow, 120 University Avenue, Glasgow G12 8TA, Scotland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.82 kDa 
• Atom Count: 4,740 
• Modelled Residue Count: 593 
• Deposited Residue Count: 616 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ ALPHA CHAIN	A, C, E, G	133	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for P18670 (Artocarpus integer) Explore P18670  Go to UniProtKB:  P18670

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ BETA-4 CHAIN	B, D, F, H	21	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for Q9S8T0 (Artocarpus integer) Explore Q9S8T0  Go to UniProtKB:  Q9S8T0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	I, J, K, L	2		N/A
Glycosylation Resources
GlyTouCan:  G00031MO GlyCosmos:  G00031MO GlyGen:  G00031MO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084	I, J, K, L	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.287	α = 90
b = 121.673	β = 90
c = 77.563	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Gabrielsen, M., Abdul-Rahman, P.S., Othman, S., Hashim, O.H., Cogdell, R.J.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary