1QGL | pdb_00001qgl

Room temperature structure of concanavalin A complexed to bivalent ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 
    0.200 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.160 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A

Dimick, S.M., Powell, S.C., Mcmahon, S.A., Moothoo, D.N., Naismith, J.H., Toone, E.J.

(1999) J Am Chem Soc 121: 10286-10296


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SUCCINYLATED CONCANAVALIN A )
A, B
237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02866
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EJT
Query on EJT
Download Ideal Coordinates CCD File 
E [auth A]1,3-DI(N-PROPYLOXY-A-MANNOPYRANOSYL)-CARBOMYL 5-METHYAZIDO-BENZENE
C27 H41 N5 O14
GKRIMQPDERYOML-LHMXEDMUSA-N
SIN
Query on SIN
Download Ideal Coordinates CCD File 
H [auth B]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free:  0.200 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.160 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.1α = 90
b = 127.4β = 90
c = 118.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-20
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Advisory, Data collection
  • Version 1.4: 2023-08-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description