4TKC

Japanese Marasmius oreades lectin complexed with mannose

• PDB DOI: https://doi.org/10.2210/pdb4TKC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Marasmius oreades
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-26 Released: 2015-06-03 
• Deposition Author(s): Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Minami, Y., Yagi, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.207 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Literature

Structure of Japanese Marasmius oreades lectin complexed with mannose.

Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Yagi, F., Minami, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 13.57 kDa 
• Atom Count: 1,067 
• Modelled Residue Count: 118 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose recognizing lectin	A	120	Marasmius oreades	Mutation(s): 0  Gene Names: Mlec1
UniProt
Find proteins for I7H471 (Marasmius oreades) Explore I7H471  Go to UniProtKB:  I7H471

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	B [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.207 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.42	α = 90
b = 58.42	β = 90
c = 57.732	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Minami, Y., Yagi, F.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Structure summary