2E7T

Crystal structure of basic winged bean lectin in complex with a blood group trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb2E7T/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Psophocarpus tetragonolobus
• Mutation(s): No 


• Deposited: 2007-01-13 Released: 2007-06-19 
• Deposition Author(s): Kulkarni, K.A., Katiyar, S., Surolia, A., Vijayan, M., Suguna, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 110.65 kDa 
• Atom Count: 7,945 
• Modelled Residue Count: 947 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic agglutinin	A, B, C, D	237	Psophocarpus tetragonolobus	Mutation(s): 0
UniProt
Find proteins for O24313 (Psophocarpus tetragonolobus) Explore O24313  Go to UniProtKB:  O24313

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I, N, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	G, J, M	3		N/A
Glycosylation Resources
GlyTouCan:  G32215KN GlyCosmos:  G32215KN GlyGen:  G32215KN

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	P [auth A], R [auth B], T [auth C], V [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	Q [auth A], S [auth B], U [auth C], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.729	α = 90
b = 91.13	β = 90
c = 73.718	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Kulkarni, K.A., Katiyar, S., Surolia, A., Vijayan, M., Suguna, K.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary