4XBH

Soluble rabbit neprilysin

• PDB DOI: https://doi.org/10.2210/pdb4XBH/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-12-16 Released: 2016-05-25 
• Deposition Author(s): Labiuk, S.L., Grochulski, P., Sygusch, J.
• Funding Organization(s): Medical Research Council (MRC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.211 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

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

• PubMed: 31204686 
• DOI: https://doi.org/10.1107/S2053230X19006046
• Primary Citation of Related Structures:  
  4XBH, 4ZR5, 5V48


• 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 2.1 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 161.64 kDa 
• Atom Count: 12,854 
• Modelled Residue Count: 1,392 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neprilysin	A, B	696	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: MME EC: 3.4.24.11
UniProt
Find proteins for P08049 (Oryctolagus cuniculus) Explore P08049  Go to UniProtKB:  P08049

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	H [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.211 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.361	α = 90
b = 108.142	β = 90
c = 212.784	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Labiuk, S.L., Grochulski, P., Sygusch, J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, Canada)	Canada	--

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-06-26
  Changes: Data collection, Database references
• Version 1.3: 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
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary