3QLQ | pdb_00003qlq

Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster

PDB DOI: https://doi.org/10.2210/pdb3QLQ/pdb

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

Deposited: 2011-02-03 Released: 2012-02-08
Deposition Author(s): Sundberg, E.J., Bonsor, D.A., Trastoy, B., Chiara, J.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Synthesis and Biophysical Study of Disassembling Nano hybrid Bioconjugates with a Cubic Octasilsesquioxane Core

Trastoy, B., Bonsor, D.A., Perez-Ojeda, M.E., Sundberg, E.J., Jimeno, M.L., Garcia-Fernandez, J.M., Chiara, J.L.

(2012) Adv Funct Mater 22: 3191-3201

DOI: https://doi.org/10.1002/adfm.201200423

Macromolecule Content

Total Structure Weight: 103.59 kDa
Atom Count: 7,466
Modeled Residue Count: 939
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 cathartica	Mutation(s): 0
UniProt
Find proteins for P81461 (Canavalia cathartica) Explore P81461 Go to UniProtKB: P81461
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81461
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain O [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C]	F [auth A], H [auth B], K [auth C], O [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [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 L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], I [auth B], L [auth C], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.89	α = 90
b = 63.68	β = 93.23
c = 125.8	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2012-08-22
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.5: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

3QLQ | pdb_00003qlq

Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster

Literature

Synthesis and Biophysical Study of Disassembling Nano hybrid Bioconjugates with a Cubic Octasilsesquioxane Core

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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