5F0E

Murine endoplasmic reticulum alpha-glucosidase II

PDB DOI: https://doi.org/10.2210/pdb5F0E/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-11-27 Released: 2016-07-27
Deposition Author(s): Caputo, A.T., Roversi, P., Alonzi, D.S., Kiappes, J.L., Zitzmann, N.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.169
R-Value Work: 0.141
R-Value Observed: 0.143

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 110.09 kDa
Atom Count: 8,720
Modelled Residue Count: 945
Deposited Residue Count: 945
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral alpha-glucosidase AB	A	857	Mus musculus	Mutation(s): 0 Gene Names: Ganab, G2an, Kiaa0088 EC: 3.2.1.84
UniProt
Find proteins for Q8BHN3 (Mus musculus) Explore Q8BHN3 Go to UniProtKB: Q8BHN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8BHN3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosidase 2 subunit beta	B	88	Mus musculus	Mutation(s): 0 Gene Names: Prkcsh
UniProt & NIH Common Fund Data Resources
Find proteins for O08795 (Mus musculus) Explore O08795 Go to UniProtKB: O08795
IMPC: MGI:107877
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O08795
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain O [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	X [auth B], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.169
R-Value Work: 0.141
R-Value Observed: 0.143
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.144	α = 90
b = 173.773	β = 90
c = 62.836	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	097300/Z/11/Z

Revision History (Full details and data files)

Version 1.0: 2016-07-27
Type: Initial release
Version 1.1: 2016-08-03
Changes: Database references
Version 1.2: 2016-08-24
Changes: Database references
Version 1.3: 2017-08-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary