2CY6 | pdb_00002cy6

Crystal structure of ConM in complex with trehalose and maltose

PDB DOI: https://doi.org/10.2210/pdb2CY6/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Canavalia rosea
Mutation(s): No

Deposited: 2005-07-05 Released: 2006-06-13
Deposition Author(s): Cavada, B.S., Azevedo Jr., W.F., Delatorre, P., Rocha, B.A.M., Souza, E.P., Gadelha, C.A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of a lectin from Canavalia maritima (ConM) in complex with trehalose and maltose reveals relevant mutation in ConA-like lectins

Delatorre, P., Rocha, B.A.M., Gadelha, C.A.A., Santi-Gadelha, T., Cajazeiras, J.B., Souza, E.P., Nascimento, K.S., Freire, V.N., Sampaio, A.H., Azevedo Jr., W.F., Cavada, B.S.

(2006) J Struct Biol 154: 280-286

PubMed: 16677825 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2006.03.011
Primary Citation Related Structures:
2CY6, 2CYF

PubMed Abstract:
The crystal structure of Canavalia maritima lectin (ConM) complexed with trehalose and maltose revealed relevant point mutations in ConA-like lectins. ConM with the disaccharides and other ConA-like lectins complexed with carbohydrates demonstrated significant differences in the position of H-bonds. The main difference in the ConM structure is the replacement of Pro202 by Ser202, a residue that promotes the approximation of Tyr12 to the carbohydrate-binding site. The O-6' of the second glucose ring in maltose interacts with Tyr12, while in trehalose the interaction is established by the O-2' and Tyr12, explaining the higher affinity of ConM for disaccharides compared to monosaccharides.

Organizational Affiliation

Departamento de Bioquímica e Biologia Molecular--Universidade Federal do Ceará, Brazil.

Macromolecule Content

Total Structure Weight: 51.86 kDa
Atom Count: 3,852
Modeled Residue Count: 474
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B [auth D]	237	Canavalia rosea	Mutation(s): 0
UniProt
Find proteins for P81460 (Canavalia lineata) Explore P81460 Go to UniProtKB: P81460
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81460
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	C [auth B], D [auth C]	2		N/A	Interactions Focus chain C [auth B] Focus chain D [auth C] Interactions & Density Focus chain C [auth B] Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D]	F [auth A], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth D]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	C [auth B], D [auth C]	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain C [auth B] Focus chain D [auth C] Interactions & Density Focus chain C [auth B] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.243 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.033	α = 90
b = 97.332	β = 90
c = 71.086	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-13
Changes: Data collection, Database references, Structure summary