3FMR

Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.183 

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This is version 1.5 of the entry. See complete history


Literature

Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470.

Alvarado, J.J.Nemkal, A.Sauder, J.M.Russell, M.Akiyoshi, D.E.Shi, W.Almo, S.C.Weiss, L.M.

(2009) Mol Biochem Parasitol 168: 158-167

  • DOI: https://doi.org/10.1016/j.molbiopara.2009.07.008
  • Primary Citation of Related Structures:  
    3FM3, 3FMQ, 3FMR

  • PubMed Abstract: 

    Microsporidia are protists that have been reported to cause infections in both vertebrates and invertebrates. They have emerged as human pathogens particularly in patients that are immunosuppressed and cases of gastrointestinal infection, encephalitis, keratitis, sinusitis, myositis and disseminated infection are well described in the literature. While benzimidazoles are active against many species of microsporidia, these drugs do not have significant activity against Enterocytozoon bieneusi. Fumagillin and its analogues have been demonstrated to have activity invitro and in animal models of microsporidiosis and human infections due to E. bieneusi. Fumagillin and its analogues inhibit methionine aminopeptidase type 2. Encephalitozoon cuniculi MetAP2 (EcMetAP2) was cloned and expressed as an active enzyme using a baculovirus system. The crystal structure of EcMetAP2 was determined with and without the bound inhibitors fumagillin and TNP-470. This structure classifies EcMetAP2 as a member of the MetAP2c family. The EcMetAP2 structure was used to generate a homology model of the E. bieneusi MetAP2. Comparison of microsporidian MetAP2 structures with human MetAP2 provides insights into the design of inhibitors that might exhibit specificity for microsporidian MetAP2.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2
A, B
358Encephalitozoon cuniculiMutation(s): 0 
Gene Names: ECU10_0750MAP2
EC: 3.4.11.18
UniProt
Find proteins for Q8SR45 (Encephalitozoon cuniculi (strain GB-M1))
Explore Q8SR45 
Go to UniProtKB:  Q8SR45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8SR45
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TN4
Query on TN4

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate
C19 H30 Cl N O6
OUUSPVSSNHLIGE-AGYLCKTBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TN4 PDBBind:  3FMR IC50: 10.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.977α = 90
b = 94.067β = 99.33
c = 66.407γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-31
    Changes: Non-polymer description
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2021-02-10
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2023-09-06
    Changes: Data collection, Database references, Refinement description