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), 0.201 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.175 (DCC) 

Starting Model: experimental
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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

Macromolecule Content 

  • Total Structure Weight: 52.21 kDa 
  • Atom Count: 3,747 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 474 
  • Unique protein chains: 1

Macromolecules

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|  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
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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), 0.201 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.175 (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

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Ligand Structure Quality Assessment 


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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