5FIC

Open form of murine Acid Sphingomyelinase in presence of lipid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 5FIC

Classification: HYDROLASE

Total Structure Weight: 247546.34

Macromolecule Entities
Molecule Chains Length Organism Details
Sphingomyelin phosphodiesterase A, B, C, D 538 Mus musculus EC#: 3.1.4.12 IUBMB
Fragment: UNP residues 84-611
Gene Name(s): Smpd1 Asm
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6E0
Query on 6E0

A, D octadecylphosphonic acid
C18 H39 O3 P
FTMKAMVLFVRZQX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

A, D ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.189
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 101.75 α = 90.00
b = 101.75 β = 90.00
c = 401.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-12-22
  • Released Date: 2016-07-06
  • Deposition author(s): Gorelik, A., Illes, K., Heinz, L.X., Superti-Furga, G., Nagar, B.

Revision History

  • 2016-08-03
    Type: Database references