5HCA

Globular Domain of the Entamoeba histolytica calreticulin in complex with glucose

PDB DOI: https://doi.org/10.2210/pdb5HCA/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Entamoeba histolytica HM-1:IMSS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-04 Released: 2016-08-31
Deposition Author(s): Moreau, C.P., Gaboriaud, C.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 95.34 kDa
Atom Count: 6,818
Modelled Residue Count: 795
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calreticulin,Calreticulin	A [auth C], B [auth A], C [auth B]	274	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0
UniProt
Find proteins for P83003 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P83003 Go to UniProtKB: P83003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P83003
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	E [auth C], G [auth A], H [auth A], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain D [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B]	D [auth C], I [auth A], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth C] Focus chain I [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B]	J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.36	α = 90
b = 143.44	β = 90
c = 171.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-08-31

Deposition Author(s):

Moreau, C.P.

Gaboriaud, C.

Funding Organization	Location	Grant Number
French National Research Agency	France	09-PIRI-0021

Revision History (Full details and data files)

Version 1.0: 2016-08-31
Type: Initial release
Version 1.1: 2016-11-09
Changes: Database references
Version 1.2: 2016-12-21
Changes: Database references
Version 1.3: 2017-09-06
Changes: Advisory, Author supporting evidence
Version 1.4: 2019-06-12
Changes: Data collection, Structure summary
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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Help and Resources

5HCA

Globular Domain of the Entamoeba histolytica calreticulin in complex with glucose

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)