5FIB

Open form of murine Acid Sphingomyelinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 5FIB

Classification: HYDROLASE

Total Structure Weight: 129796.13

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
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)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 2.8 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.190
  • Space Group: P 4 21 2

Unit Cell:

Length (Å) Angle (°)
a = 181.17 α = 90.00
b = 181.17 β = 90.00
c = 109.89 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

  • Version 1_0: 2016-07-06

    Type: Initial release

  • Version 1_1: 2016-08-03

    Type: Database references