5Z5L | pdb_00005z5l

Crystal structure of ConA-R5M

• PDB DOI: https://doi.org/10.2210/pdb5Z5L/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia ensiformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-18 Released: 2019-04-10 
• Deposition Author(s): Hu, R.T., Gan, J.H., Chen, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.277 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of ConA-R5M

Hu, R.T., Gan, J.H., Chen, G.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 103.14 kDa 
• Atom Count: 7,155 
• Modeled Residue Count: 919 
• 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
96O	I [auth B]	(1-methyl-1H-1,2,3-triazol-4-yl)methyl alpha-D-mannopyranoside C10 H17 N3 O6 GTGCGDYGALMCDQ-ZJDVBMNYSA-N
MN	E [auth A], G [auth B], J [auth C], L [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	F [auth A], H [auth B], K [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.277 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.415	α = 90
b = 64.086	β = 92.9
c = 126.106	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Hu, R.T., Gan, J.H., Chen, G.S.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-03-27
  Changes: Advisory, Data collection, Database references, Structure summary