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- PDB-5jmy: NEPRILYSIN COMPLEXED WITH LBQ657 -

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Basic information

Entry
Database: PDB / ID: 5jmy
TitleNEPRILYSIN COMPLEXED WITH LBQ657
ComponentsNeprilysin
KeywordsHYDROLASE / LBQ657 / sacubitril / heart failure
Function / homology
Function and homology information


neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / amygdala development / exopeptidase activity / substance P catabolic process / Physiological factors / cellular response to UV-A / amyloid-beta clearance by cellular catabolic process ...neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / amygdala development / exopeptidase activity / substance P catabolic process / Physiological factors / cellular response to UV-A / amyloid-beta clearance by cellular catabolic process / peptide metabolic process / hormone catabolic process / bradykinin catabolic process / cardiolipin binding / cellular response to UV-B / positive regulation of neurogenesis / phosphatidylserine binding / cellular response to cytokine stimulus / neuron projection terminus / Developmental Lineage of Mammary Gland Myoepithelial Cells / amyloid-beta clearance / brush border / replicative senescence / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / peptide binding / lung development / sensory perception of pain / secretory granule membrane / placenta development / protein catabolic process / positive regulation of long-term synaptic potentiation / hippocampus development / kidney development / trans-Golgi network / protein processing / metalloendopeptidase activity / response to estrogen / multicellular organism growth / memory / synaptic vesicle / presynapse / cytoplasmic vesicle / endopeptidase activity / learning or memory / early endosome / ciliary basal body / membrane raft / axon / focal adhesion / neuronal cell body / Neutrophil degranulation / centrosome / synapse / dendrite / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Collagenase (Catalytic Domain) ...Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / 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
Sacubitrilat / Neprilysin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchiering, N. / Wiesmann, C.
CitationJournal: Sci Rep / Year: 2016
Title: Structure of neprilysin in complex with the active metabolite of sacubitril.
Authors: Schiering, N. / D'Arcy, A. / Villard, F. / Ramage, P. / Logel, C. / Cumin, F. / Ksander, G.M. / Wiesmann, C. / Karki, R.G. / Mogi, M.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
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 / diffrn_radiation_wavelength / 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.ptnr1_label_asym_id / _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 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neprilysin
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,58514
Polymers159,5112
Non-polymers3,07412
Water16,033890
1
A: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2937
Polymers79,7561
Non-polymers1,5376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2937
Polymers79,7561
Non-polymers1,5376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.737, 109.139, 248.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Common acute lymphocytic leukemia antigen / CALLA / Enkephalinase / Neutral ...Atriopeptidase / Common acute lymphocytic leukemia antigen / CALLA / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin fibroblast elastase / SFE


Mass: 79755.680 Da / Num. of mol.: 2 / Fragment: UNP residues 53-750
Source method: isolated from a genetically manipulated source
Details: LBQ657 - the active metabolite of sacubitril, contained in Entresto (sacubitril/valsartan)
Source: (gene. exp.) Homo sapiens (human) / Gene: MME, EPN / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08473, neprilysin

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Sugars , 2 types, 8 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.: 2
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
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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, 894 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-6LD / Sacubitrilat / LBQ657


Mass: 383.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 6.5, 25% W/V PEG 3350. 2 MM MGCL2 AND PROTEIN SOLUTION WERE MIXED

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→82.65 Å / Num. obs: 108554 / % possible obs: 98.2 % / Redundancy: 4 % / Biso Wilson estimate: 34.15 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.75
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.62 / % possible all: 97.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.11.6refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DMT

1dmt


Resolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4992 4.6 %RANDOM
Rwork0.186 ---
obs0.188 108529 98.2 %-
Displacement parametersBiso mean: 42.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.8639 Å20 Å20 Å2
2---0.8565 Å20 Å2
3----0.0075 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11190 0 198 890 12278
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111666HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0615809HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4173SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes360HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1659HARMONIC5
X-RAY DIFFRACTIONt_it11666HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion19.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1518SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14406SEMIHARMONIC4
LS refinement shellHighest resolution: 2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.267 362 4.6 %
Rwork0.236 7505 -
obs--97.66 %

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