2KR2 | pdb_00002kr2

Xenopus laevis malectin complexed with maltose (Glcalpha1-4Glc)

• PDB DOI: https://doi.org/10.2210/pdb2KR2/pdb

• Classification: carbohydrate binding protein
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-30 Released: 2010-07-14 
• Deposition Author(s): Schallus, T., Feher, K., Muhle-Goll, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 

Literature

Analysis of the specific interactions between the lectin domain of malectin and diglucosides.

Schallus, T., Feher, K., Sternberg, U., Rybin, V., Muhle-Goll, C.

(2010) Glycobiology 20: 1010-1020

• PubMed: 20466650 
• DOI: https://doi.org/10.1093/glycob/cwq059
• Primary Citation Related Structures: 
  2KR2


• PubMed Abstract: 
  

  The endoplasmic reticulum malectin is a highly conserved protein in the animal kingdom that has no counterpart so far in lower organisms. We recently determined the structure of its conserved domain and found a highly selective binding to Glc(2)Man(9)GlcNAc(2), an intermediate of N-glycosylation. In our quest for putative ligands during the initial characterization of the protein, we noticed that the malectin domain is highly specific for diglucosides but quite tolerant towards the linkage of the glucosidic bond. To understand the molecular requirements for the observed promiscuity of the malectin domain, here we analyze the binding to a range of diglucosides through comparison of the protein chemical shift perturbation patterns and the saturation transfer difference spectra of the ligands including two maltose-mimicking drugs. A comparison of the maltose-bound structure of the malectin domain with the complex of the native ligand nigerose reveals why malectin is able to tolerate such a diversity of ligands.

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Organizational Affiliation: 
• EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.54 kDa 
• Atom Count: 1,517 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malectin-A	A	190	Xenopus laevis	Mutation(s): 0  Gene Names: mlec, mlec-A
UniProt
Find proteins for Q6INX3 (Xenopus laevis) Explore Q6INX3  Go to UniProtKB:  Q6INX3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G66120GK GlyCosmos: G66120GK

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018	B	beta-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Schallus, T., Feher, K., Muhle-Goll, C.

Revision History  

• Version 1.0: 2010-07-14
  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, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Structure summary