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- PDB-5e3a: Structure of human DPP3 in complex with opioid peptide leu-enkephalin -

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Basic information

Entry
Database: PDB / ID: 5e3a
TitleStructure of human DPP3 in complex with opioid peptide leu-enkephalin
Components
  • Dipeptidyl peptidase 3DPP3
  • Leu-enkephalin
KeywordsHYDROLASE / Peptide-complex / Zinc-hydrolase / opioid-peptide / 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 / G protein-coupled opioid receptor signaling pathway / symmetric synapse / cell body fiber / response to epinephrine / sensory perception / cellular response to vitamin D / neuropeptide hormone activity / metalloexopeptidase activity / dipeptidyl-peptidase activity / locomotory exploration behavior / transmission of nerve impulse / startle response / neuropeptide signaling pathway / behavioral fear response / glial cell proliferation / axon terminus / aminopeptidase activity / cellular response to cAMP / sensory perception of pain / cellular response to transforming growth factor beta stimulus / Peptide ligand-binding receptors / response to nicotine / Post-translational protein phosphorylation / protein catabolic process / response to toxic substance / osteoblast differentiation / cellular response to virus / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / KEAP1-NFE2L2 pathway / response to estradiol / cellular response to oxidative stress / Neddylation / G alpha (i) signalling events / chemical synaptic transmission / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / endoplasmic reticulum lumen / dendrite / neuronal cell body / signal transduction / proteolysis / extracellular exosome / zinc ion binding / extracellular region / plasma membrane / cytosol / cytoplasm
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: 2.05 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 2, 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 / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,2576
Polymers82,1042
Non-polymers1534
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-63 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.558, 105.757, 64.992
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1189-

HOH

21A-1239-

HOH

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Components

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

#1: Protein Dipeptidyl peptidase 3 / DPP3 / 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 Leu-enkephalin


Mass: 555.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: opioid peptide from human source / Source: (synth.) Homo sapiens (human) / References: UniProt: P01210*PLUS

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Non-polymers , 4 types, 367 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 / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 1.344M POTASSIUM PHOSPHATE DIBASIC
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: 2.05→39.58 Å / Num. all: 48267 / Num. obs: 48267 / % possible obs: 95.09 % / Redundancy: 3 % / Biso Wilson estimate: 32.96 Å2 / Rmerge(I) obs: 0.08875 / Rsym value: 0.08875 / Net I/σ(I): 10.73
Reflection shellResolution: 2.05→2.121 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6197 / Mean I/σ(I) obs: 1.85 / % possible all: 95.45

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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: 2.05→39.576 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / ESU R: 0.2088 / ESU R Free: 0.259 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 2405 5 %Random selection
Rwork0.2088 ---
obs0.2113 48113 94.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.2 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 4 363 6157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025936
X-RAY DIFFRACTIONf_angle_d0.6168038
X-RAY DIFFRACTIONf_dihedral_angle_d12.9142188
X-RAY DIFFRACTIONf_chiral_restr0.024865
X-RAY DIFFRACTIONf_plane_restr0.0031055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08930.35361390.30452626X-RAY DIFFRACTION93
2.0893-2.13480.33891460.29312785X-RAY DIFFRACTION98
2.1348-2.18440.36021450.29842752X-RAY DIFFRACTION98
2.1844-2.2390.39011230.352319X-RAY DIFFRACTION82
2.239-2.29960.40481020.37241939X-RAY DIFFRACTION69
2.2996-2.36720.34021430.29662710X-RAY DIFFRACTION96
2.3672-2.44360.31191440.28012732X-RAY DIFFRACTION97
2.4436-2.5310.29051460.24932773X-RAY DIFFRACTION97
2.531-2.63230.27041460.22892792X-RAY DIFFRACTION99
2.6323-2.7520.29251480.22842810X-RAY DIFFRACTION99
2.752-2.89710.24981470.21922795X-RAY DIFFRACTION99
2.8971-3.07850.26061500.21272838X-RAY DIFFRACTION99
3.0785-3.31610.26971480.20992820X-RAY DIFFRACTION99
3.3161-3.64960.27151460.19412774X-RAY DIFFRACTION97
3.6496-4.17720.23271350.17192589X-RAY DIFFRACTION91
4.1772-5.26090.19451480.15132811X-RAY DIFFRACTION99
5.2609-39.5830.19481490.15582843X-RAY DIFFRACTION98

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