7W4B | pdb_00007w4b

Phloem lectin (PP2) structure -complex with Chitotrise

• PDB DOI: https://doi.org/10.2210/pdb7W4B/pdb

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


• Deposited: 2021-11-26 Released: 2023-03-08 
• Deposition Author(s): Sivaji, N., Kishore, B.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: 2.50 Å
• R-Value Free: 
  0.297 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.282 (Depositor) 
• R-Value Observed: 
  0.283 (Depositor) 

Starting Model: experimental

Literature

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

Sivaji, N., Kishore, B.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: Asymmetric - C1 
Global Stoichiometry: Homo 12-mer - A12 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local 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: 214.56 kDa 
• Atom Count: 14,835 
• Modeled Residue Count: 1,752 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17 kDa phloem lectin	A, B, C, D, E, F, G, H, I, J, K, L	150	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	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, O, P, Q, R, S, T, U, V, W, X [auth Y]	3		N/A
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	M, N, O, P, Q, R, S, T, U, V, W, X [auth Y]	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.297 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.282 (Depositor) 
• R-Value Observed: 0.283 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.29	α = 90
b = 92.41	β = 90
c = 280.78	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., Kishore, B.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 2.0: 2024-05-22
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-16
  Changes: Structure summary