3NWK | pdb_00003nwk

A second C2221 form of concanavalin A (Canavalia ensiformis)

PDB DOI: https://doi.org/10.2210/pdb3NWK/pdb

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

Deposited: 2010-07-09 Released: 2011-07-13
Deposition Author(s): Foroughi, L.M., Kang, Y.N., Matzger, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.212 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

Foroughi, L.M., Kang, Y.N., Matzger, A.J.

(2011) Cryst Growth Des 11: 1294-1298

DOI: https://doi.org/10.1021/cg101518f

Macromolecule Content

Total Structure Weight: 103.88 kDa
Atom Count: 7,827
Modeled Residue Count: 948
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B, C, D	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866 Go to UniProtKB: P02866
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02866
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	G [auth A] H [auth A] K [auth B] L [auth B] M [auth B] G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	F [auth A], J [auth B], P [auth C], U [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	E [auth A], I [auth B], O [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.212 (Depositor), 0.222 (DCC)
R-Value Work: 0.176 (Depositor), 0.190 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.518	α = 90
b = 118.118	β = 90
c = 250.113	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Foroughi, L.M.

Kang, Y.N.

Matzger, A.J.

Revision History (Full details and data files)

Version 1.0: 2011-07-13
Type: Initial release
Version 1.1: 2017-07-05
Changes: Source and taxonomy
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description