5FI9

Closed form of murine Acid Sphingomyelinase in complex with bisphosphonate inhibitor AbPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 5FI9

Classification: HYDROLASE / HYDROLASE Inhibitor

Total Structure Weight: 127642.88

Macromolecule Entities
Molecule Chains Length Organism Details
Sphingomyelin phosphodiesterase A, B 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 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NT8
Query on NT8

A, B (1-azanyl-1-phosphono-decyl)phosphonic acid
C10 H25 N O6 P2
TWYYYYAFACTHMV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

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

A, B 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: 2.54 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.201
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 57.39 α = 80.47
b = 72.02 β = 71.52
c = 74.42 γ = 83.60

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