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- PDB-5v48: Soluble rabbit neprilysin in complex with thiorphan -

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Basic information

Entry
Database: PDB / ID: 5v48
TitleSoluble rabbit neprilysin in complex with thiorphan
ComponentsNeprilysin
KeywordsHYDROLASE / Neutral Endopeptidase / Proteinase / Zn-dependent
Function / homology
Function and homology information


neprilysin / creatinine metabolic process / substance P catabolic process / peptide metabolic process / cellular response to UV-A / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / cellular response to UV-B / cellular response to cytokine stimulus ...neprilysin / creatinine metabolic process / substance P catabolic process / peptide metabolic process / cellular response to UV-A / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / cellular response to UV-B / cellular response to cytokine stimulus / brush border / replicative senescence / amyloid-beta metabolic process / sensory perception of pain / kidney development / peptide binding / metalloendopeptidase activity / synaptic vesicle / axon / dendrite / synapse / proteolysis / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Neprilysin-like (M13) protease domain profile. / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Collagenase (Catalytic Domain) ...Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Neprilysin-like (M13) protease domain profile. / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE / Neprilysin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9965 Å
AuthorsLabiuk, S.L. / Grochulski, P. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structures of soluble rabbit neprilysin complexed with phosphoramidon or thiorphan.
Authors: Labiuk, S.L. / Sygusch, J. / Grochulski, P.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neprilysin
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,95713
Polymers158,9592
Non-polymers2,99911
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-74 kcal/mol
Surface area57100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.994, 108.446, 211.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neprilysin / / Atriopeptidase / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin ...Atriopeptidase / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin fibroblast elastase / SFE


Mass: 79479.359 Da / Num. of mol.: 2 / Fragment: UNP Residues 67-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: MME / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / Variant (production host): his4- / References: UniProt: P08049, neprilysin

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Sugars , 2 types, 7 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 740 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TIO / (2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE / THIORPHAN / Thiorphan


Mass: 253.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO3S / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe sequence from GB XP_008264403.1 matches the experimental electron density

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG4000, magnesium chloride, sodium cacodylate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.996→40 Å / Num. obs: 27886 / % possible obs: 85.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 38.71 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.915 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID% possible all
3-3.110.20222451.112171.7
3.11-3.230.1490.975182.1
3.23-3.380.1210.951188.1
3.38-3.560.10.933190.8
3.56-3.780.0770.841164.7
3.78-4.070.0580.831174.4
4.07-4.480.0470.882195.9
4.48-5.130.0430.837196.5
5.13-6.460.0461.05195.7
6.46-400.030.866191

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xbh

4xbh


Resolution: 2.9965→39.471 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.2446 1997 7.18 %
Rwork0.195 --
obs0.1986 27862 79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.95 Å2 / Biso mean: 45.1209 Å2 / Biso min: 6.37 Å2
Refinement stepCycle: final / Resolution: 2.9965→39.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11182 0 190 736 12108
Biso mean--66.98 31.53 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411643
X-RAY DIFFRACTIONf_angle_d0.37715766
X-RAY DIFFRACTIONf_chiral_restr0.0371709
X-RAY DIFFRACTIONf_plane_restr0.0032048
X-RAY DIFFRACTIONf_dihedral_angle_d9.6516978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9965-3.03750.3676870.31081154124151
3.0375-3.08090.351150.27581373148860
3.0809-3.12690.28861210.26661515163666
3.1269-3.17570.31821160.2511550166669
3.1757-3.22770.33241250.24451653177872
3.2277-3.28340.29331320.24341787191976
3.2834-3.34310.28881410.23281814195581
3.3431-3.40730.23971560.22241987214385
3.4073-3.47680.30371480.21421901204983
3.4768-3.55240.25421590.21971988214789
3.5524-3.6350.3051540.21251970212485
3.635-3.72580.185370.199550354022
3.7258-3.82650.28221600.20292045220589
3.8265-3.9390.2746620.192484490637
3.939-4.0660.24881530.18392102225590
4.066-4.21110.20931580.17882089224792
4.2111-4.37950.21731660.16852132229893
4.3795-4.57860.21091610.15682140230193
4.5786-4.81960.19141630.16852121228494
4.8196-5.12090.21211650.16632154231994
5.1209-5.51540.24851640.17892122228693
5.5154-6.06860.23561700.18082135230593
6.0686-6.94260.23571730.1842103227693
6.9426-8.73130.18771620.16812088225091
8.7313-39.47420.20421480.17871945209385

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