5KAR
Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)
- PDB DOI: https://doi.org/10.2210/pdb5KAR/pdb
- Classification: HYDROLASE
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2016-06-02 Released: 2016-10-05 
- Funding Organization(s): Canadian Institutes of Health Research (CIHR)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.14 Å
- R-Value Free: 0.152 
- R-Value Work: 0.135 
- R-Value Observed: 0.136 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Acid sphingomyelinase-like phosphodiesterase 3b | 427 | Mus musculus | Mutation(s): 0  Gene Names: Smpdl3b, Asml3b EC: 3.1.4 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P58242 (Mus musculus) Explore P58242  Go to UniProtKB:  P58242 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P58242 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GOL Query on GOL | I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | E [auth A], F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
NO3 Query on NO3 | G [auth A], H [auth A] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.14 Å
- R-Value Free: 0.152 
- R-Value Work: 0.135 
- R-Value Observed: 0.136 
- Space Group: P 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 50.892 | α = 90 |
b = 47.031 | β = 98.07 |
c = 93.861 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-10-05  Deposition Author(s): Gorelik, A., Illes, K., Heinz, L.X., Superti-Furga, G., Nagar, B.
Funding Organization | Location | Grant Number |
---|---|---|
Canadian Institutes of Health Research (CIHR) | Canada | MOP-133535 |
Revision History (Full details and data files)
- Version 1.0: 2016-10-05
Type: Initial release - Version 1.1: 2016-10-12
Changes: Database references - Version 1.2: 2016-11-23
Changes: Database references - Version 1.3: 2020-01-08
Changes: Author supporting evidence, Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary