5ZAC | pdb_00005zac

Crystal structure of ConA-R2M

PDB DOI: https://doi.org/10.2210/pdb5ZAC/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Canavalia ensiformis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-07 Released: 2018-05-30
Deposition Author(s): Gan, J.H., Chen, G.S., Hu, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.372 (Depositor), 0.369 (DCC)
R-Value Work:
0.278 (Depositor), 0.280 (DCC)
R-Value Observed:
0.283 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Competition between Supramolecular Interaction and Protein-Protein Interaction in Protein Crystallization:Effects of Crystallization Method and Small Molecular Bridge

Hu, R.T., Yang, G., Ding, H.M., Ma, J.B., Ma, Y.Q., Gan, J.H., Chen, G.S.

(2018) Ind Eng Chem Res 57: 6726-6733

DOI: https://doi.org/10.1021/acs.iecr.8b00657

Macromolecule Content

Total Structure Weight: 103.51 kDa
Atom Count: 7,348
Modeled Residue Count: 924
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain L [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth C]	L [auth C], Q [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain L [auth C] Focus chain Q [auth D]
TA5 Query on TA5 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C]	M [auth C], R [auth D]	2H-1,2,3-TRIAZOL-4-YLMETHANOL C₃ H₅ N₃ O OADYBXHYXPEGHX-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain M [auth C] Focus chain R [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C], N [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain N [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] K [auth C] O [auth D] F [auth A], G [auth A], I [auth B], K [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.372 (Depositor), 0.369 (DCC)
R-Value Work: 0.278 (Depositor), 0.280 (DCC)
R-Value Observed: 0.283 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.227	α = 90
b = 119.893	β = 90
c = 125.211	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Gan, J.H.

Chen, G.S.

Hu, R.T.

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-03-27
Changes: Data collection, Database references, Structure summary