8ZE7 | pdb_00008ze7

Crystal Structure of Concanavalin A Complexed with Lysine

• PDB DOI: https://doi.org/10.2210/pdb8ZE7/pdb

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


• Deposited: 2024-05-04 Released: 2025-05-07 
• Deposition Author(s): Rasheed, S., Arif, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Concanavalin A Complexed with Lysine

Rasheed, S., Arif, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 25.96 kDa 
• Atom Count: 1,924 
• Modeled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-Br	A	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P55915 (Canavalia brasiliensis) Explore P55915  Go to UniProtKB:  P55915

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS (Subject of Investigation/LOI)	B [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.926	α = 90
b = 86.214	β = 90
c = 88.428	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Rasheed, S., Arif, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release