4P9X | pdb_00004p9x

Structure of ConA/Rh3Glu complex

• PDB DOI: https://doi.org/10.2210/pdb4P9X/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 2014-04-06 Released: 2014-08-27 
• Deposition Author(s): Sakai, F., Weiss, M.S., Chen, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.295 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Structure of ConA/Rh3Glu complex

Sakai, F., Weiss, F.S., Chen, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 106.15 kDa 
• Atom Count: 7,594 
• Modeled Residue Count: 948 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B, C, D	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866  Go to UniProtKB:  P02866

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R3G	E [auth A], H [auth B], K [auth C], N [auth D]	2-[2-(2-{4-[(alpha-D-glucopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate C43 H57 N5 O11 LPSYXQPVOZLKRL-OUZFDYGBSA-N
MN	F [auth A], I [auth B], L [auth C], O [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	G [auth A], J [auth B], M [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.295 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.173	α = 90
b = 116.028	β = 95.98
c = 84.255	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Sakai, F., Weiss, M.S., Chen, G.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description