4ZR5

Soluble rabbit neprilysin in complex with phosphoramidon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 F Struct Biol Commun 75: 405-411

  • DOI: 10.1107/S2053230X19006046
  • Primary Citation of Related Structures:  
    5V48, 4ZR5, 4XBH

  • 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 extracellular domain (residues 55-750) of rabbit neprilysin was solved both in its native form at 2 ...

    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

    Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeprilysinA, B696Oryctolagus cuniculusMutation(s): 0 
Gene Names: MME
EC: 3.4.24.11
Find proteins for P08049 (Oryctolagus cuniculus)
Explore P08049 
Go to UniProtKB:  P08049
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D, E, F2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RDF
Query on RDF

Download Ideal Coordinates CCD File 
H [auth A], K [auth B]N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A], L [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A], J [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDFIC50:  27   nM  BindingDB
RDFIC50:  26   nM  BindingDB
RDFIC50:  6   nM  BindingDB
RDFIC50:  0.4000000059604645   nM  BindingDB
RDFIC50:  4.199999809265137   nM  BindingDB
RDFIC50:  30   nM  BindingDB
RDFIC50:  100   nM  BindingDB
RDFKi:  4   nM  BindingDB
RDFIC50:  0.6000000238418579   nM  BindingDB
RDFIC50:  30   nM  BindingDB
RDFIC50:  200   nM  BindingDB
RDFIC50:  2   nM  BindingDB
RDFIC50:  2   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
H [auth A], K [auth B]PHOSPHORAMIDONGlycopeptide /  Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.513α = 90
b = 107.446β = 90
c = 210.589γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Non-polymer description
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.4: 2019-11-13
    Changes: Database references
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary