1HQW | pdb_00001hqw

CRYSTAL STRUCTURE OF THE COMPLEX OF CONCANAVALIN A WITH A TRIPEPTIDE YPY

• PDB DOI: https://doi.org/10.2210/pdb1HQW/pdb

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


• Deposited: 2000-12-20 Released: 2003-10-07 
• Deposition Author(s): Zhang, Z., Qian, M., Huang, Q., Jia, Y., Tang, Y., Wang, K., Cui, D., Li, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structure of the complex of concanavalin A and tripeptide

Zhang, Z., Qian, M., Huang, Q., Jia, Y., Tang, Y., Wang, K., Cui, D., Li, M.

(2001) J Protein Chem 20: 59-65

• PubMed: 11330349 
• DOI: https://doi.org/10.1023/a:1011053330536
• Primary Citation Related Structures: 
  1HQW


• PubMed Abstract: 
  

  The X-ray structure analysis of a cross-linked crystal of concanavalin A soaked with the tripeptide molecule as the probe molecule showed electron density corresponding to full occupation in the binding pocket. The site lies on the surface of concanavalin A and is surrounded by three symmetry-related molecules. The crystal structure of the tripeptide complex was refined at 2.4-A resolution to an R-factor of 17.5%, (Rfree factor of 23.7%), with an RMS deviation in bond distances of 0.01 A. The model includes all 237 residue of concanavalin A, 1 manganese ion, 1 calcium ion, 161 water molecules, 1 glutaraldehyde molecule, and 1 tripeptide molecule. This X-ray structure analysis also provides an approach to mapping the binding surface of crystalline protein with a probe molecule that is dissolved in a mixture of organic solvent with water or in neat organic solvent but is hardly dissolved in aqueous solution.

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Organizational Affiliation: 
• Department of Chemistry, Peking University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.26 kDa 
• Atom Count: 1,967 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YPY	B	3	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTD	E [auth A]	PENTANEDIAL C5 H8 O2 SXRSQZLOMIGNAQ-UHFFFAOYSA-N
MN	C [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: 2.40 Å
• R-Value Free:  0.237 (Depositor) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.63	α = 90
b = 86.57	β = 90
c = 89.29	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-07 
Deposition Author(s): Zhang, Z., Qian, M., Huang, Q., Jia, Y., Tang, Y., Wang, K., Cui, D., Li, M.

Revision History  

• Version 1.0: 2003-10-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations