5TCD

Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 5TCD

Classification: HYDROLASE

Total Structure Weight: 55748.12

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 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)
PC
Query on PC

A PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
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)
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: 2.4 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.173
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 104.22 α = 90.00
b = 104.22 β = 90.00
c = 113.89 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-09-14
  • Released Date: 2017-03-22
  • Deposition author(s): Gorelik, A., Liu, F., Illes, K., Nagar, B.

Revision History

  • 2017-05-10
    Type: Database references