Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.80 kDa 
• Atom Count: 4166 
• Modelled Residue Count: 480 
• Deposited Residue Count: 504 
• Unique protein chains: 1

2PHW

Pterocarpus angolensis lectin (PAL) in complex with Man-9

• PDB DOI: 10.2210/pdb2PHW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pterocarpus angolensis
• Mutation(s): No 


• Deposited: 2007-04-12 Released: 2007-07-10 
• Deposition Author(s): Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.175 

Literature

How a plant lectin recognizes high mannose oligosaccharides

Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.

(2007) Plant Physiol 144: 1733-1741

• PubMed: 17556509 
• DOI: 10.1104/pp.107.100867
• Primary Citation of Related Structures:  
  2PHF, 2PHR, 2PHT, 2PHU, 2PHW, 2PHX


• PubMed Abstract: 
  

The crystal structure of Pterocarpus angolensis seed lectin is presented in complex with a series of high mannose (Man) oligosaccharides ranging from Man-5 to Man-9. Despite that several of the nine Man residues of Man-9 have the potential to bind in the monosaccharide-binding site, all oligomannoses are bound in the same unique way, employing the tetrasaccharide sequence Manalpha(1-2)Manalpha(1-6)[Manalpha(1-3)]Manalpha(1-. Isothermal titration calorimetry titration experiments using Man-5, Man-9, and the Man-9-containing glycoprotein soybean (Glycine max) agglutinin as ligands confirm the monovalence of Man-9 and show a 4-times higher affinity for Man-9 when it is presented to P. angolensis seed lectin in a glycoprotein context.

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Organizational Affiliation: 

Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	252	Pterocarpus angolensis	Mutation(s): 0
UniProt
Find proteins for Q8GSD2 (Pterocarpus angolensis) Explore Q8GSD2  Go to UniProtKB:  Q8GSD2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G00891MP GlyCosmos:  G00891MP GlyGen:  G00891MP

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose	D	7		N/A
Glycosylation Resources
GlyTouCan:  G53708VP GlyCosmos:  G53708VP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	F [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112	C	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.694	α = 90
b = 83.205	β = 90
c = 122.919	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-12 
• Released Date: 2007-07-10 
Deposition Author(s): Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.

Revision History  

• Version 1.0: 2007-07-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 2.0: 2019-12-25
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary