4R6P

Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.

• PDB DOI: https://doi.org/10.2210/pdb4R6P/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Artocarpus integer
• Mutation(s): No 


• Deposited: 2014-08-26 Released: 2015-02-18 
• Deposition Author(s): Abhinav, K.V., Sharma, K., Swaminathan, C.P., Surolia, A., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.11 kDa 
• Atom Count: 5,071 
• Modelled Residue Count: 594 
• Deposited Residue Count: 608 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin alpha chain	A, C, E, G	133	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for P18670 (Artocarpus integer) Explore P18670  Go to UniProtKB:  P18670

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin beta-3 chain	B, D, F, H	19	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for P18673 (Artocarpus integer) Explore P18673  Go to UniProtKB:  P18673

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	O [auth G]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
ZZ1	N [auth G]	4-METHYL-2H-CHROMEN-2-ONE C10 H8 O2 PSGQCCSGKGJLRL-UHFFFAOYSA-N
EDO	L [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	I [auth A], J [auth A], K [auth C], M [auth E]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.53	α = 90
b = 80.88	β = 107.88
c = 63.04	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Abhinav, K.V., Sharma, K., Swaminathan, C.P., Surolia, A., Vijayan, M.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Data collection, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary