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- PDB-5e33: Structure of human DPP3 in complex with met-enkephalin -

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Basic information

Entry
Database: PDB / ID: 5.0E+33
TitleStructure of human DPP3 in complex with met-enkephalin
Components
  • Dipeptidyl peptidase 3
  • Met-enkephalin
KeywordsHYDROLASE / Complex / Opioid-peptide / Zinc-hydrolase / peptidase
Function / homology
Function and homology information


synaptic vesicle lumen / neuronal dense core vesicle lumen / dipeptidyl-peptidase III / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response ...synaptic vesicle lumen / neuronal dense core vesicle lumen / dipeptidyl-peptidase III / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response / symmetric synapse / G protein-coupled opioid receptor signaling pathway / response to epinephrine / cell body fiber / sensory perception / cellular response to vitamin D / neuropeptide hormone activity / metalloexopeptidase activity / dipeptidyl-peptidase activity / startle response / transmission of nerve impulse / locomotory exploration behavior / response to immobilization stress / behavioral fear response / neuropeptide signaling pathway / glial cell proliferation / aminopeptidase activity / axon terminus / cellular response to cAMP / sensory perception of pain / cellular response to transforming growth factor beta stimulus / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to nicotine / protein catabolic process / response to toxic substance / cellular response to virus / response to calcium ion / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / KEAP1-NFE2L2 pathway / response to estradiol / Neddylation / cellular response to oxidative stress / G alpha (i) signalling events / chemical synaptic transmission / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / endoplasmic reticulum lumen / neuronal cell body / dendrite / signal transduction / proteolysis / zinc ion binding / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Proenkephalin A / Dipeptidyl-peptidase 3 / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature. / Peptidase family M49 / Peptidase family M49 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 ...Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Proenkephalin A / Dipeptidyl-peptidase 3 / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature. / Peptidase family M49 / Peptidase family M49 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Proenkephalin-A / Dipeptidyl peptidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å
AuthorsKumar, P. / Reithofer, V. / Reisinger, M. / Pavkov-Keller, T. / Wallner, S. / Macheroux, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Sci Rep / Year: 2016
Title: Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition.
Authors: Kumar, P. / Reithofer, V. / Reisinger, M. / Wallner, S. / Pavkov-Keller, T. / Macheroux, P. / Gruber, K.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 3.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
B: Met-enkephalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2756
Polymers82,1222
Non-polymers1534
Water9,350519
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-63 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.790, 105.760, 65.167
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1180-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Dipeptidyl peptidase 3 / Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / ...Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / Enkephalinase B


Mass: 81548.688 Da / Num. of mol.: 1 / Mutation: C19S, E207C, E451A, S491C, C519S, C654S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3 / Plasmid: PET28MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NY33, dipeptidyl-peptidase III
#2: Protein/peptide Met-enkephalin


Mass: 573.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01210*PLUS

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Non-polymers , 4 types, 523 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phospahte dibasic, pH- 8.2
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.83→45.42 Å / Num. all: 68276 / Num. obs: 68276 / % possible obs: 96.86 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.13 Å2 / Rmerge(I) obs: 0.05052 / Rsym value: 0.05052 / Net I/σ(I): 14.78
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.75 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6B

3t6b


Resolution: 1.837→45.416 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3411 5 %Random selection
Rwork0.1815 ---
obs0.1836 68229 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 1.837→45.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 4 519 6313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115957
X-RAY DIFFRACTIONf_angle_d1.1758070
X-RAY DIFFRACTIONf_dihedral_angle_d14.6222204
X-RAY DIFFRACTIONf_chiral_restr0.056867
X-RAY DIFFRACTIONf_plane_restr0.0061061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8375-1.86370.33781370.2842606X-RAY DIFFRACTION92
1.8637-1.89160.31011380.31162605X-RAY DIFFRACTION95
1.8916-1.92110.43281270.3492415X-RAY DIFFRACTION87
1.9211-1.95260.37041330.30732530X-RAY DIFFRACTION90
1.9526-1.98630.26551410.24432691X-RAY DIFFRACTION98
1.9863-2.02240.27461420.22052681X-RAY DIFFRACTION97
2.0224-2.06130.261410.21912690X-RAY DIFFRACTION96
2.0613-2.10340.30021410.21822665X-RAY DIFFRACTION95
2.1034-2.14910.21721430.19512732X-RAY DIFFRACTION99
2.1491-2.19910.2511440.18462725X-RAY DIFFRACTION99
2.1991-2.25410.26021340.20932551X-RAY DIFFRACTION92
2.2541-2.3150.24421410.19192664X-RAY DIFFRACTION96
2.315-2.38320.24361460.17912783X-RAY DIFFRACTION99
2.3832-2.46010.25011450.18422751X-RAY DIFFRACTION98
2.4601-2.5480.20751440.18712743X-RAY DIFFRACTION99
2.548-2.650.23241470.18452788X-RAY DIFFRACTION99
2.65-2.77060.22681440.19692743X-RAY DIFFRACTION98
2.7706-2.91660.23891460.19522764X-RAY DIFFRACTION100
2.9166-3.09930.25891460.19052783X-RAY DIFFRACTION99
3.0993-3.33860.20561450.17972748X-RAY DIFFRACTION99
3.3386-3.67440.23491450.17152760X-RAY DIFFRACTION99
3.6744-4.20580.18631470.15422778X-RAY DIFFRACTION98
4.2058-5.29750.17551470.14632800X-RAY DIFFRACTION100
5.2975-45.430.17811470.15072822X-RAY DIFFRACTION99

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