7VWB

Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)

• PDB DOI: https://doi.org/10.2210/pdb7VWB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cucumis sativus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-10 Released: 2023-03-08 
• Deposition Author(s): Sivaji, N., Bobbili, K.B., Suguna, K., Surolia, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 

Starting Model: experimental

Literature

Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus.

Sivaji, N., Bobbili, K.B., Suguna, K., Surolia, A.

(2023) Structure 31: 1-16

• DOI: https://doi.org/10.1016/j.str.2023.02.008

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 36.13 kDa 
• Atom Count: 2,718 
• Modelled Residue Count: 300 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phloem lectin	A, B	154	Cucumis sativus	Mutation(s): 0  Gene Names: Lec17-7
UniProt
Find proteins for Q8LK69 (Cucumis sativus) Explore Q8LK69  Go to UniProtKB:  Q8LK69

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G79333MY GlyCosmos:  G79333MY GlyGen:  G79333MY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900019	C, D	N-acetyl-alpha-lactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.69	α = 90
b = 60.39	β = 99.13
c = 82.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Sivaji, N., Bobbili, K.B., Suguna, K., Surolia, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary