5KAR

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.135

Literature

Macromolecules
Sequence Display for 5KAR

Classification: HYDROLASE

Total Structure Weight: 51193.42

Macromolecule Entities
Molecule Chains Length Organism Details
Acid sphingomyelinase-like phosphodiesterase 3b A 427 Mus musculus EC#: 3.1.4 IUBMB
Fragment: UNP residues 19-435
Gene Name(s): Smpdl3b Asml3b
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.135
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 50.89 α = 90.00
b = 47.03 β = 98.07
c = 93.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-02
  • Released Date: 2016-10-05
  • Deposition author(s): Gorelik, A., Illes, K., Heinz, L.X., Superti-Furga, G., Nagar, B.

Revision History

  • 2016-10-12
    Type: Database references
  • 2016-11-23
    Type: Database references