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- PDB-2yb9: Crystal Structure of Human Neutral Endopeptidase complexed with a... -

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Basic information

Entry
Database: PDB / ID: 2yb9
TitleCrystal Structure of Human Neutral Endopeptidase complexed with a heteroarylalanine diacid.
ComponentsNEPRILYSIN
KeywordsHYDROLASE / NEPRILYSINE / METALLOPROTEINASE
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 / phosphatidylserine binding / cellular response to UV-B / 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 / metalloendopeptidase activity / protein processing / response to estrogen / synaptic vesicle / presynapse / cytoplasmic vesicle / endopeptidase activity / learning or memory / early endosome / membrane raft / axon / focal adhesion / dendrite / neuronal cell body / synapse / 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
HETEROARYLALANINE 5-PHENYL OXAZOLE / Neprilysin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsGlossop, M.S. / Bazin, R.J. / Dack, K.N. / Done, S. / Fox, D.N.A. / MacDonald, G.A. / Mills, M. / Owen, D.R. / Phillips, C. / Reeves, K.A. ...Glossop, M.S. / Bazin, R.J. / Dack, K.N. / Done, S. / Fox, D.N.A. / MacDonald, G.A. / Mills, M. / Owen, D.R. / Phillips, C. / Reeves, K.A. / Ringer, T.J. / Strang, R.S. / Watson, C.A.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Synthesis and Evaluation of Heteroarylalanine Diacids as Potent and Selective Neutral Endopeptidase Inhibitors.
Authors: Glossop, M.S. / Bazin, R.J. / Dack, K.N. / Fox, D.N.A. / Macdonald, G.A. / Mills, M. / Owen, D.R. / Phillips, C. / Reeves, K.A. / Ringer, T.J. / Strang, R.S. / Watson, C.A.L.
History
DepositionMar 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references / Version format compliance

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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)80,0333
Polymers79,5261
Non-polymers5082
Water8,683482
1
A: NEPRILYSIN
hetero molecules

A: NEPRILYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,0676
Polymers159,0512
Non-polymers1,0164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1920 Å2
ΔGint-13.5 kcal/mol
Surface area55460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.841, 107.841, 112.794
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 / ATRIOPEPTIDASE / COMMON ACUTE LYMPHOCYTIC LEUKEMIA ANTIGEN / CALLA / ...NEUTRAL ENDOPEPTIDASE / ATRIOPEPTIDASE / COMMON ACUTE LYMPHOCYTIC LEUKEMIA ANTIGEN / CALLA / ENKEPHALINASE / NEUTRAL ENDOPEPTIDASE 24.11 / NEP / NEUTRAL ENDOPEPTIDASE / SKIN FIBROBLAST ELASTASE / SFE / CD10


Mass: 79525.508 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08473, neprilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HA0 / HETEROARYLALANINE 5-PHENYL OXAZOLE


Mass: 442.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N2O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.34 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29854 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.59 % / Biso Wilson estimate: 39.39 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5

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Processing

SoftwareName: BUSTER / Version: 2.9.6 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→31.13 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.8979 / SU R Cruickshank DPI: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.549 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.264 / Details: GLYCOSYLATION NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1516 5.08 %RANDOM
Rwork0.1723 ---
obs0.1758 29846 99.27 %-
Displacement parametersBiso mean: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.6395 Å20 Å20 Å2
2---1.6395 Å20 Å2
3---3.2791 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 33 482 6110
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.157780HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2027SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes186HARMONIC2
X-RAY DIFFRACTIONt_gen_planes817HARMONIC5
X-RAY DIFFRACTIONt_it5749HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion20.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
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_contact7037SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3003 129 4.54 %
Rwork0.188 2715 -
all0.1926 2844 -
obs--99.27 %

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