5I8R

aSMase with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.

Zhou, Y.F.Metcalf, M.C.Garman, S.C.Edmunds, T.Qiu, H.Wei, R.R.

(2016) Nat Commun 7: 13082-13082

  • DOI: https://doi.org/10.1038/ncomms13082
  • Primary Citation of Related Structures:  
    5I81, 5I85, 5I8R

  • PubMed Abstract: 

    Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann-Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.


  • Organizational Affiliation

    Protein Engineering Department, Biologics Research, Sanofi, Framingham, Massachusetts 01701, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingomyelin phosphodiesterase
A, B, C
583Homo sapiensMutation(s): 0 
Gene Names: SMPD1ASM
EC: 3.1.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P17405 (Homo sapiens)
Explore P17405 
Go to UniProtKB:  P17405
PHAROS:  P17405
GTEx:  ENSG00000166311 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17405
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
J [auth A]
K [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
J [auth A],
K [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
P [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
L [auth A],
W [auth B]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
Q [auth A]
R [auth A]
X [auth B]
DA [auth C],
EA [auth C],
Q [auth A],
R [auth A],
X [auth B],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.02α = 90
b = 230.87β = 90
c = 252.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary