5IEG

Murine endoplasmic reticulum alpha-glucosidase II with N-9'-methoxynonyl-1-deoxynojirimycin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutral alpha-glucosidase AB914Mus musculusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BHN3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosidase 2 subunit beta88Mus musculusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08795
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6A9
Query on 6A9
Download Ideal Coordinates CCD File 
D [auth A] N-9'-methoxynonyl-1-deoxynojirimycin
C16 H33 N O5
TYTARGBBJQKLAJ-QKPAOTATSA-N
P6G
Query on P6G
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J [auth A],
K [auth A],
L [auth A],
P [auth A]		HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4
Query on PG4
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N [auth A],
O [auth A],
S [auth B]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
DMS
Query on DMS
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M [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT
Query on FMT
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E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.321α = 90
b = 173.311β = 90
c = 63.032γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom097300/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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary