4ZR5 | pdb_00004zr5

Soluble rabbit neprilysin in complex with phosphoramidon

• PDB DOI: https://doi.org/10.2210/pdb4ZR5/pdb

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


• Deposited: 2015-05-11 Released: 2016-06-08 
• 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: 2.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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 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.
Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, QC H3C 3J7, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.32 kDa 
• Atom Count: 11,669 
• Modeled 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
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
RDF	H [auth A], K [auth B]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C23 H34 N3 O10 P ZPHBZEQOLSRPAK-XLCYBJAPSA-N
NAG	I [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	G [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000638 (RDF)	H [auth A], K [auth B]	PHOSPHORAMIDON	Glycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.513	α = 90
b = 107.446	β = 90
c = 210.589	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-08 
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: 2016-06-08
  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
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary