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- PDB-4zr5: Soluble rabbit neprilysin in complex with phosphoramidon -

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Basic information

Entry
Database: PDB / ID: 4zr5
TitleSoluble rabbit neprilysin in complex with phosphoramidon
ComponentsNeprilysin
KeywordsHYDROLASE / Neutral Endopeptidase / Phosphoramidon / Zn-dependent
Function / homology
Function and homology information


neprilysin / creatinine metabolic process / substance P catabolic process / cellular response to UV-A / peptide metabolic process / 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 / cellular response to UV-A / peptide metabolic process / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / cellular response to UV-B / cellular response to cytokine stimulus / amyloid-beta clearance / brush border / replicative senescence / amyloid-beta metabolic process / sensory perception of pain / peptide binding / kidney development / metalloendopeptidase activity / protein processing / synaptic vesicle / axon / synapse / dendrite / proteolysis / zinc ion binding / plasma membrane / cytoplasm
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
PHOSPHORAMIDON / Chem-RDF / Neprilysin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.8016 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
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Non-polymer description
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jun 26, 2019Group: Data collection / Database references / Category: citation
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
Revision 1.4Nov 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 1.5Jan 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_molecule / 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_molecule.asym_id / _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 2.1Sep 27, 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)162,31712
Polymers158,9592
Non-polymers3,35810
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1586
Polymers79,4791
Non-polymers1,6795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1586
Polymers79,4791
Non-polymers1,6795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.513, 107.446, 210.589
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: MME / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / Variant (production host): his4- / References: UniProt: P08049, neprilysin

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Sugars , 2 types, 6 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 275 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-RDF / N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN / PHOSPHORAMIDON


Type: peptide-like, Glycopeptide / Class: Enzyme inhibitor / Mass: 543.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34N3O10P / References: PHOSPHORAMIDON / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe sequence from GB XP_008264403.1 matches the experimental electron density
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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, magnesium chloride, sodium cacodylate; 1 hr soak in 0.2 mM phosphoramidon

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 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: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 33003 / % possible obs: 84.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 30.78 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.029 / Net I/av σ(I): 16.37 / Net I/σ(I): 14.3 / Num. measured all: 84480
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-IDRejects% possible all
2.8-2.90.16517621.211045.7
2.9-3.020.12822591.1231059.1
3.02-3.150.11230111.0781078.1
3.15-3.320.0934141.0131088.3
3.32-3.530.06935150.9911090.9
3.53-3.80.05536600.9041093.8
3.8-4.180.04537550.9311096.6
4.18-4.790.0438590.9881098.3
4.79-6.030.04438971.161097.8
6.03-400.03338841.0391093.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: 4XBH

4xbh


Resolution: 2.8016→39.213 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3384 6.11 %Random selection
Rwork0.1917 52021 --
obs0.1939 33003 75.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.6 Å2 / Biso mean: 33.4488 Å2 / Biso min: 9.04 Å2
Refinement stepCycle: final / Resolution: 2.8016→39.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11182 0 216 271 11669
Biso mean--45.36 24.48 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411662
X-RAY DIFFRACTIONf_angle_d0.90115792
X-RAY DIFFRACTIONf_chiral_restr0.0371716
X-RAY DIFFRACTIONf_plane_restr0.0032046
X-RAY DIFFRACTIONf_dihedral_angle_d12.2194298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8016-2.84160.2965630.254974103734
2.8416-2.8840.3004770.25841127120439
2.884-2.9290.3358820.24761258134044
2.929-2.9770.3115850.25341386147147
2.977-3.02830.34351110.2311512162354
3.0283-3.08340.32141150.23261749186461
3.0834-3.14270.26531340.22842045217970
3.1427-3.20680.26621260.22392113223973
3.2068-3.27650.25951440.22582154229874
3.2765-3.35270.24891430.2242178232176
3.3527-3.43650.25541420.20842249239177
3.4365-3.52930.25731520.20042252240479
3.5293-3.63310.21391610.212341250280
3.6331-3.75030.24721570.18952370252783
3.7503-3.88420.21871570.17972440259785
3.8842-4.03960.22311640.17232521268587
4.0396-4.22320.2171640.16492599276390
4.2232-4.44560.18581690.1622643281292
4.4456-4.72370.16431700.14682746291694
4.7237-5.08770.20771750.16692687286294
5.0877-5.59840.22321830.18482738292195
5.5984-6.40540.20081750.19812713288894
6.4054-8.05860.21861780.20522704288294
8.0586-39.21660.18571570.17882522267987

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