4AKD

High resolution structure of Mannose Binding lectin from Champedak (CMB)

• PDB DOI: https://doi.org/10.2210/pdb4AKD/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: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

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: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 65.85 kDa 
• Atom Count: 4,832 
• Modelled Residue Count: 594 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE-SPECIFIC LECTIN KM+	A, B, C, D	150	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for Q7M1T4 (Artocarpus integer) Explore Q7M1T4  Go to UniProtKB:  Q7M1T4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A], F [auth B], G [auth B], H [auth B], M [auth C], N [auth C], R [auth C], S [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	I [auth B], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.887	α = 90
b = 86.222	β = 90
c = 95.373	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 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description