1QGL

Room temperature structure of concanavalin A complexed to bivalent ligand

PDB DOI: https://doi.org/10.2210/pdb1QGL/pdb

Classification: LECTIN (AGGLUTININ)
Organism(s): Canavalia ensiformis
Mutation(s): No

Deposited: 1999-04-30 Released: 1999-05-20
Deposition Author(s): Naismith, J.H.

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
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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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUCCINYLATED CONCANAVALIN A )	A, B	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866 Go to UniProtKB: P02866
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02866
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EJT Query on EJT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,3-DI(N-PROPYLOXY-A-MANNOPYRANOSYL)-CARBOMYL 5-METHYAZIDO-BENZENE C₂₇ H₄₁ N₅ O₁₄ GKRIMQPDERYOML-LHMXEDMUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

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 = 99.1	α = 90
b = 127.4	β = 90
c = 118.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-05-20

Deposition Author(s):

Naismith, J.H.

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