1XXR

Structure of a mannose-specific jacalin-related lectin from Morus Nigra in complex with mannose

• PDB DOI: https://doi.org/10.2210/pdb1XXR/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Morus nigra
• Mutation(s): No 


• Deposited: 2004-11-08 Released: 2005-10-25 
• Deposition Author(s): Rabijns, A., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J., Rouge, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Literature

Structural analysis of the jacalin-related lectin MornigaM from the black mulberry (Morus nigra) in complex with mannose

Rabijns, A., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J., Rouge, P.

(2005) FEBS J 272: 3725-3732

• PubMed: 16008570 
• DOI: https://doi.org/10.1111/j.1742-4658.2005.04801.x
• Primary Citation of Related Structures:  
  1XXQ, 1XXR


• PubMed Abstract: 
  

  The structures of MornigaM and the MornigaM-mannose complex have been determined at 1.8 A and 2.0 A resolution, respectively. Both structures adopt the typical beta-prism motif found in other jacalin-related lectins and their tetrameric assembly closely resembles that of jacalin. The carbohydrate-binding cavity of MornigaM readily binds mannose. No major structural rearrangements can be observed in MornigaM upon binding of mannose. These results allow corroboration of the structure-function relationships within the small group of Moraceae lectins.

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Organizational Affiliation: 

Laboratory of Analytical Chemistry and Medicinal Physicochemistry, Faculty of Pharmaceutical Sciences, K. U. Leuven, Belgium.

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: 69.05 kDa 
• Atom Count: 5,223 
• Modelled Residue Count: 616 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mannose-binding lectin	A, B, C, D	161	Morus nigra	Mutation(s): 0
UniProt
Find proteins for Q8LGR3 (Morus nigra) Explore Q8LGR3  Go to UniProtKB:  Q8LGR3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	G [auth B], I [auth C], K [auth D]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	E [auth A], J [auth C], L [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.908	α = 90
b = 110.908	β = 90
c = 160.021	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Rabijns, A., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J., Rouge, P.

Revision History  

• Version 1.0: 2005-10-25
  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 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Structure summary