5J50

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

• PDB DOI: https://doi.org/10.2210/pdb5J50/pdb

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


• Deposited: 2016-04-01 Released: 2017-02-08 
• Deposition Author(s): Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.
• Funding Organization(s): Department of Science and Technology, Govt. of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.

To be published.

Biological Assembly 1  

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 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)

Macromolecule Content

• Total Structure Weight: 69.41 kDa 
• Atom Count: 5,143 
• 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	I, J, K, L	2		N/A
Glycosylation Resources
GlyTouCan:  G00031MO GlyCosmos:  G00031MO GlyGen:  G00031MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPO	BA [auth G], P [auth A], Q [auth C], Y [auth E]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
PEG	V [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	AA [auth G], CA [auth H], M [auth A], N [auth A], O [auth A], R [auth C], S [auth C], T [auth C], U [auth C], W [auth E], X [auth E], Z [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084	I, J, K, L	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.53	α = 90
b = 81.65	β = 100
c = 66.89	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: 2017-02-08 
Deposition Author(s): Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.

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Funding Organization	Location	Grant Number
Department of Science and Technology, Govt. of India	India	--

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary