Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 112.23 kDa 
• Atom Count: 7772 
• Modelled Residue Count: 928 
• Deposited Residue Count: 944 
• Unique protein chains: 1

1RIT

Crystal structure of Peanut lectin in complex with meso-tetrasulphonatophenylporphyrin and lactose

• PDB DOI: 10.2210/pdb1RIT/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Arachis hypogaea
• Mutation(s): No 


• Deposited: 2003-11-17 Released: 2004-12-28 
• Deposition Author(s): Goel, M., Kaur, K.J., Maiya, B.G., Swamy, M.J., Salunke, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 

Literature

Crystal structures of the PNA-porphyrin complex in the presence and absence of lactose: mapping the conformational changes on lactose binding, interacting surfaces, and supramolecular aggregations.

Goel, M., Damai, R.S., Sethi, D.K., Kaur, K.J., Maiya, B.G., Swamy, M.J., Salunke, D.M.

(2005) Biochemistry 44: 5588-5596

• PubMed: 15823017 
• DOI: 10.1021/bi047377s
• Primary Citation of Related Structures:  
  1RIR, 1RIT


• PubMed Abstract: 
  

The extraordinary recognition specificity of lectins for carbohydrate ligands appears to be violated as they also bind to porphyrins and other noncarbohydrate ligands. In this study, crystal structures of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) bound to peanut agglutinin (PNA) in the presence and absence of lactose were determined. The binding of H(2)TPPS with PNA involved 11 molecules of H(2)TPPS in different supramolecular stacking arrangements associated with a tetramer of PNA in the crystals of the PNA-H(2)TPPS binary complex as well as the PNA-H(2)TPPS-lactose ternary complex. The ternary complex involved lactose binding only to two subunits of the PNA tetramer, which did not have porphyrin interacting in the vicinity of the carbohydrate-binding site. Comparison of the two structures highlighted the plasticity of the carbohydrate-binding site expressed in terms of the conformational change in lactose binding. The unusual quaternary structure of PNA, which results in exposed protein-protein interaction sites, might be responsible for the porphyrin binding. The association of porphyrin in diverse oligomeric stacking arrangements observed in the PNA-H(2)TPPS complex suggested the possibility of protein-porphyrin aggregation under abnormal physiological conditions. The structures described here provide a possible native conformation of the carbohydrate-binding site of PNA in the absence of the ligand, highlight mapping of the unsaturated binding surfaces of PNA using porphyrin interactions, indicate new leads toward possible application of this lectin in photodynamic therapy, and exhibit diverse modes of porphyrin-lectin interactions with implications to porphyria, a disease that results from abnormal accumulation of porphyrins.

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Related Citations: 

• Functional equality in the absence of structural similarity: an added dimension to molecular mimicry.
  Goel, M., Jain, D., Kaur, K.J., Kenoth, R., Maiya, B.G., Swamy, M.J., Salunke, D.M.
  (2001) J Biol Chem 276: 39277

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Organizational Affiliation: 

National Institute of Immunology, New Delhi 110067, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding lectin	A, B, C, D	236	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for P02872 (Arachis hypogaea) Explore P02872  Go to UniProtKB:  P02872

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFP	G [auth A], H [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D]	5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE C44 H34 N4 O12 S4 OVPFWIRROXFHGQ-LWQDQPMZSA-J
MN	J [auth A], Q [auth B], U [auth C], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth A], P [auth B], T [auth C], X [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	E, F	beta-lactose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.9	α = 90
b = 94.9	β = 90
c = 144.1	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-17 
• Released Date: 2004-12-28 
Deposition Author(s): Goel, M., Kaur, K.J., Maiya, B.G., Swamy, M.J., Salunke, D.M.

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary