4P9Y

Structure of ConA/Rh4man

PDB DOI: https://doi.org/10.2210/pdb4P9Y/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Canavalia ensiformis
Mutation(s): No

Deposited: 2014-04-06 Released: 2014-08-27
Deposition Author(s): Sakai, F., Weiss, M.S., Chen, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.258
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of ConA/Rh4Man

Sakai, F., Weiss, M.S., Chen, G.

To be published.

Macromolecule Content

Total Structure Weight: 53.16 kDa
Atom Count: 3,839
Modelled Residue Count: 474
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KO Query on 2KO 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]	C [auth A], F [auth B]	2-{2-[2-(2-{4-[(alpha-D-mannopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethoxy}ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate C₄₅ H₆₁ N₅ O₁₂ NMXJNHVQXYBXDU-ZOLSBRMLSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MN Query on MN 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]	D [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.258
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 116.11	β = 90
c = 58.69	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
Coot	model building
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Sakai, F.

Weiss, M.S.

Chen, G.

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release
Version 1.1: 2017-11-22
Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4P9Y

Structure of ConA/Rh4man

Structure of ConA/Rh4Man

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)