1JOT

STRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb1JOT/pdb

• Classification: LECTIN
• Organism(s): Maclura pomifera
• Mutation(s): No 


• Deposited: 1997-12-05 Released: 1998-12-30 
• Deposition Author(s): Lee, X., Thompson, A., Zhang, Z., Hoa, T.-T., Biesterfeldt, J., Ogata, C., Xu, L., Johnston, R.A.Z., Young, N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 17.3 kDa 
• Atom Count: 1,283 
• Modelled Residue Count: 149 
• Deposited Residue Count: 153 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ	A	133	Maclura pomifera	Mutation(s): 0
UniProt
Find proteins for P18674 (Maclura pomifera) Explore P18674  Go to UniProtKB:  P18674

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ	B	20	Maclura pomifera	Mutation(s): 0
UniProt
Find proteins for P18676 (Maclura pomifera) Explore P18676  Go to UniProtKB:  P18676

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	C	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	C	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.6	α = 90
b = 67.6	β = 90
c = 149.26	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SOFTWARE	data reduction
HAMLIN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-30 
Deposition Author(s): Lee, X., Thompson, A., Zhang, Z., Hoa, T.-T., Biesterfeldt, J., Ogata, C., Xu, L., Johnston, R.A.Z., Young, N.M.

Revision History  

• Version 1.0: 1998-12-30
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-04-03
  Changes: Refinement description