4ZR5

Soluble rabbit neprilysin in complex with phosphoramidon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8016 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structures of soluble rabbit neprilysin complexed with phosphoramidon or thiorphan.

Labiuk, S.L.Sygusch, J.Grochulski, P.

(2019) Acta Crystallogr.,Sect.F 75: 405-411

  • DOI: 10.1107/S2053230X19006046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Neutral endopeptidase (neprilysin; NEP) is a proteinase that cleaves a wide variety of peptides and has been implicated in Alzheimer's disease, cardiovascular conditions, arthritis and other inflammatory diseases. The structure of the soluble extrace ...

    Neutral endopeptidase (neprilysin; NEP) is a proteinase that cleaves a wide variety of peptides and has been implicated in Alzheimer's disease, cardiovascular conditions, arthritis and other inflammatory diseases. The structure of the soluble extracellular domain (residues 55-750) of rabbit neprilysin was solved both in its native form at 2.1 Å resolution, and bound to the inhibitors phosphoramidon and thiorphan at 2.8 and 3.0 Å resolution, respectively. Consistent with the extracellular domain of human neprilysin, the structure reveals a large central cavity which contains the active site and the location for inhibitor binding.


    Organizational Affiliation

    Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, QC H3C 3J7, Canada.,Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neprilysin
A, B
696Oryctolagus cuniculusMutation(s): 0 
Gene Names: MME
EC: 3.4.24.11
Find proteins for P08049 (Oryctolagus cuniculus)
Go to Gene View: MME
Go to UniProtKB:  P08049
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download SDF File 
Download CCD File 
A, B
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
PHOSPHORAMIDON
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
A,BPHOSPHORAMIDONGlycopeptide / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDFKi: 4 nM (94) BINDINGDB
RDFIC50: 0.4 - 200 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8016 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.513α = 90.00
b = 107.446β = 90.00
c = 210.589γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, Canada)Canada--

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Non-polymer description
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-06-26
    Type: Data collection, Database references
  • Version 1.4: 2019-11-13
    Type: Database references
  • Version 1.5: 2020-01-08
    Type: Author supporting evidence