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- PDB-9qr8: Gliadin degrading prolyl endopeptidase Celiacase (neprosin C334V) -

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Basic information

Entry
Database: PDB / ID: 9qr8
TitleGliadin degrading prolyl endopeptidase Celiacase (neprosin C334V)
ComponentsProtein neprosin
KeywordsHYDROLASE / protease / prolyl endopeptidase / glutamate-class
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Neprosin / Neprosin activation peptide / : / Neprosin / Neprosin activation peptide / Neprosin prolyl endopeptidase (PEP) catalytic domain profile.
Similarity search - Domain/homology
GLYCINE / DI(HYDROXYETHYL)ETHER / Protein neprosin
Similarity search - Component
Biological speciesNepenthes alata x Nepenthes ventricosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRodriguez-Banqueri, A. / Eckhard, U. / Gomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Structure of Celiacase at 1.90 Angstroms resolution
Authors: Rodriguez-Banqueri, A. / Eckhard, U. / Gomis-Ruth, F.X.
#1: Journal: Nat Commun / Year: 2022
Title: Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy.
History
DepositionApr 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein neprosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,36414
Polymers40,5481
Non-polymers1,81713
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.010, 39.580, 64.640
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein neprosin / Npr1 / Prolyl endopeptidase


Mass: 40547.816 Da / Num. of mol.: 1 / Mutation: C334V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nepenthes alata x Nepenthes ventricosa (plant)
Production host: Homo sapiens (human) / References: UniProt: C0HLV2, prolyl oligopeptidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 196 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium sulphate, 0.1 M Bis-Tris propane (pH 6.5) and 22% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.9→61.44 Å / Num. obs: 21884 / % possible obs: 96.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→2.01 Å / Rmerge(I) obs: 0.158 / Num. unique obs: 21336 / Rrim(I) all: 0.186

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→61.44 Å / SU ML: 0.3233 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.6289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 529 2.42 %
Rwork0.2097 21336 -
obs0.2108 21865 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 116 185 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752151
X-RAY DIFFRACTIONf_angle_d0.90152935
X-RAY DIFFRACTIONf_chiral_restr0.0573307
X-RAY DIFFRACTIONf_plane_restr0.0079378
X-RAY DIFFRACTIONf_dihedral_angle_d15.6434731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.36121250.31124769X-RAY DIFFRACTION87.13
2.09-2.390.33411420.26655419X-RAY DIFFRACTION99.11
2.39-3.020.30071370.23425501X-RAY DIFFRACTION99.45
3.02-61.440.19361250.16775647X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 1.71458246424 Å / Origin y: 7.45628834245 Å / Origin z: 20.2196657679 Å
111213212223313233
T0.299521213146 Å20.00281047525902 Å20.0241514828899 Å2-0.256018631796 Å20.0100234881592 Å2--0.262123972232 Å2
L1.03164913994 °20.0196474818213 °20.384135578466 °2-0.610650239447 °2-0.0716605454734 °2--1.20291373815 °2
S-0.00585786933834 Å °-0.00114998797717 Å °0.0172887564484 Å °-0.0347072629903 Å °0.0382909854671 Å °0.056699023248 Å °-0.0655105208806 Å °-0.100391918375 Å °-0.000473767378571 Å °
Refinement TLS groupSelection details: all

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