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- PDB-1r1i: STRUCTURAL ANALYSIS OF NEPRILYSIN WITH VARIOUS SPECIFIC AND POTEN... -

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Basic information

Entry
Database: PDB / ID: 1r1i
TitleSTRUCTURAL ANALYSIS OF NEPRILYSIN WITH VARIOUS SPECIFIC AND POTENT INHIBITORS
ComponentsNeprilysin
KeywordsHYDROLASE / LT1_9 / glycoprotein
Function / homology
Function and homology information


neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / exopeptidase activity / Physiological factors / substance P catabolic process / peptide metabolic process / cellular response to UV-A / amyloid-beta clearance by cellular catabolic process ...neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / exopeptidase activity / Physiological factors / substance P catabolic process / peptide metabolic process / cellular response to UV-A / amyloid-beta clearance by cellular catabolic process / cardiolipin binding / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / positive regulation of neurogenesis / cellular response to UV-B / phosphatidylserine binding / amyloid-beta clearance / cellular response to cytokine stimulus / brush border / replicative senescence / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / sensory perception of pain / secretory granule membrane / placenta development / kidney development / positive regulation of long-term synaptic potentiation / peptide binding / lung development / protein catabolic process / trans-Golgi network / protein processing / metalloendopeptidase activity / response to estrogen / synaptic vesicle / presynapse / cytoplasmic vesicle / endopeptidase activity / learning or memory / early endosome / membrane raft / axon / focal adhesion / neuronal cell body / synapse / dendrite / Neutrophil degranulation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / zinc ion binding / membrane / 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(R,S)-2-SULFANYLHEPTANOYL]-PHE-ALA / Neprilysin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOefner, C. / Roques, B.P. / Fournie-Zaluski, M.C. / Dale, G.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structural analysis of neprilysin with various specific and potent inhibitors.
Authors: Oefner, C. / Roques, B.P. / Fournie-Zaluski, M.C. / Dale, G.E.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6356
Polymers79,5261
Non-polymers1,1105
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.845, 108.845, 113.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Neprilysin / / Neutral endopeptidase / NEP / Enkephalinase / Common acute lymphocytic leukemia antigen / CALLA / ...Neutral endopeptidase / NEP / Enkephalinase / Common acute lymphocytic leukemia antigen / CALLA / Neutral endopeptidase 24.11 / CD10


Mass: 79525.508 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (residue 54-749)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MME OR EPN / Plasmid: PPICZ-ALPHA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YEAST / References: UniProt: P08473, neprilysin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TI1 / [2(R,S)-2-SULFANYLHEPTANOYL]-PHE-ALA


Mass: 380.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N2O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.41 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 25414 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.6
Reflection shellResolution: 2.55→2.75 Å / Rmerge(I) obs: 0.272 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.84 / SU B: 29.403 / SU ML: 0.621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35835 1186 5 %RANDOM
Rwork0.27614 ---
all0.2801 ---
obs0.28015 22350 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.364 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å21.06 Å20 Å2
2--2.12 Å20 Å2
3----3.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 69 19 5683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215790
X-RAY DIFFRACTIONr_bond_other_d0.0010.025073
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9547836
X-RAY DIFFRACTIONr_angle_other_deg0.668311845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0483695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73151037
X-RAY DIFFRACTIONr_chiral_restr0.0730.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021160
X-RAY DIFFRACTIONr_nbd_refined0.370.32217
X-RAY DIFFRACTIONr_nbd_other0.3480.36428
X-RAY DIFFRACTIONr_nbtor_other0.7340.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2880.5371
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2370.532
X-RAY DIFFRACTIONr_metal_ion_refined0.250.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.510.329
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.1150.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it4.1723461
X-RAY DIFFRACTIONr_mcangle_it6.26835572
X-RAY DIFFRACTIONr_scbond_it3.8122329
X-RAY DIFFRACTIONr_scangle_it5.76132264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.738 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.488 154
Rwork0.38 3237

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