9J1D | pdb_00009j1d

Structure of ConA/PHE-Man

• PDB DOI: https://doi.org/10.2210/pdb9J1D/pdb

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


• Deposited: 2024-08-04 Released: 2024-12-04 
• Deposition Author(s): Li, L., Chen, G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of ConA/PHE-Man

Li, L., 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.2 kDa 
• Atom Count: 3,676 
• Modeled Residue Count: 474 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B	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
A1EAW (Subject of Investigation/LOI)	C [auth A]	~{N}2,~{N}9-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]-1,10-phenanthroline-2,9-dicarboxamide C34 H46 N4 O16 OKAYCRSCTNGBEC-RYKYLIPQSA-N
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.43	α = 90
b = 141.43	β = 90
c = 80.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Li, L., Chen, G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Structure summary