6MHM

Crystal structure of human acid ceramidase in covalent complex with carmofur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.743 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular mechanism of inhibition of acid ceramidase by carmofur.

Dementiev, A.Joachimiak, A.Nguyen, H.Gorelik, A.Illes, K.Shabani, S.Gelsomino, M.Ahn, E.E.Nagar, B.Doan, N.

(2018) J. Med. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acid ceramidase subunit alpha
A, C
131Homo sapiensMutation(s): 0 
Gene Names: ASAH1 (ASAH)
EC: 3.5.1.23
Find proteins for Q13510 (Homo sapiens)
Go to Gene View: ASAH1
Go to UniProtKB:  Q13510
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acid ceramidase subunit beta
B, D
253Homo sapiensMutation(s): 0 
Gene Names: ASAH1 (ASAH)
EC: 3.5.1.23
Find proteins for Q13510 (Homo sapiens)
Go to Gene View: ASAH1
Go to UniProtKB:  Q13510
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
JRY
Query on JRY

Download SDF File 
Download CCD File 
B, D
hexylcarbamic acid
C7 H15 N O2
YAQPZDICKJDHTR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.743 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.718α = 90.00
b = 68.650β = 120.73
c = 98.386γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release