1S1A

Pterocarpus angolensis seed lectin (PAL) with one binding site free and one binding site containing the disaccharide Man(a1-3)ManMe

• PDB DOI: https://doi.org/10.2210/pdb1S1A/pdb

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


• Deposited: 2004-01-06 Released: 2005-01-18 
• Deposition Author(s): Buts, L., Imberty, A., Wyns, L., Beeckmans, S., Loris, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.66 kDa 
• Atom Count: 3,916 
• Modelled Residue Count: 482 
• Deposited Residue Count: 504 
• Unique protein chains: 1

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	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside	C	2		N/A
Glycosylation Resources
GlyTouCan:  G59594NN GlyCosmos:  G59594NN

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.868	α = 90
b = 83.212	β = 90
c = 123.23	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Buts, L., Imberty, A., Wyns, L., Beeckmans, S., Loris, R.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2021-07-21
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description