5UDY

Human alkaline sphingomyelinase (alk-SMase, ENPP7, NPP7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 5UDY

Classification: HYDROLASE

Total Structure Weight: 53418.55

Macromolecule Entities
Molecule Chains Length Organism Details
Ectonucleotide pyrophosphatase/phosphodiesterase family member 7 A 422 Homo sapiens EC#: 3.1.4.12 IUBMB
Fragment: UNP residues 22-433
Gene Name(s): ENPP7 Gene View UNQ3077/PRO9912
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 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)
FUC
Query on FUC

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

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.179
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 103.25 α = 90.00
b = 103.25 β = 90.00
c = 113.55 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-12-28
  • Released Date: 2017-03-22
  • Deposition author(s): Gorelik, A., Liu, F., Illes, K., Nagar, B.

Revision History

  • Version 1_0: 2017-03-22

    Type: Initial release

  • Version 1_1: 2017-05-10

    Type: Database references

  • Version 1_2: 2017-09-27

    Type: Author supporting evidence