5FC6

Murine SMPDL3A in complex with ADP analog AMPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.161

Literature

Macromolecules
Sequence Display for 5FC6

Classification: HYDROLASE

Total Structure Weight: 52560.13

Macromolecule Entities
Molecule Chains Length Organism Details
Acid sphingomyelinase-like phosphodiesterase 3a A 433 Mus musculus EC#: 3.1.4 IUBMB
Fragment: UNP residues 23-445
Gene Name(s): Smpdl3a Asml3a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AP2
Query on AP2

A PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H17 N5 O9 P2
OLCWZBFDIYXLAA-IOSLPCCCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.161
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 124.35 α = 90.00
b = 132.89 β = 90.00
c = 80.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-12-15
  • Released Date: 2016-01-27
  • Deposition author(s): Gorelik, A., Illes, K., Superti-Furga, G., Nagar, B.

Revision History

  • Version 1_0: 2016-01-27

    Type: Initial release

  • Version 1_1: 2016-02-03

    Type: Database references

  • Version 1_2: 2016-03-30

    Type: Database references