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- PDB-5e2q: Structure of human DPP3 in complex with angiotensin-II -

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Basic information

Entry
Database: PDB / ID: 5e2q
TitleStructure of human DPP3 in complex with angiotensin-II
Components
  • Dipeptidyl peptidase 3
  • angiotensin-II
KeywordsHYDROLASE / Complex / Peptidase / Zinc-hydrolase
Function / homology
Function and homology information


dipeptidyl-peptidase III / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / regulation of extracellular matrix assembly / regulation of renal output by angiotensin ...dipeptidyl-peptidase III / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of extracellular matrix assembly / positive regulation of branching involved in ureteric bud morphogenesis / : / type 1 angiotensin receptor binding / metalloexopeptidase activity / vasoconstriction / low-density lipoprotein particle remodeling / response to angiotensin / positive regulation of macrophage derived foam cell differentiation / dipeptidyl-peptidase activity / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of protein metabolic process / positive regulation of gap junction assembly / blood vessel remodeling / negative regulation of MAP kinase activity / regulation of cardiac conduction / regulation of vasoconstriction / aminopeptidase activity / positive regulation of epithelial to mesenchymal transition / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / positive regulation of cytokine production / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / protein catabolic process / PPARA activates gene expression / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process / positive regulation of NF-kappaB transcription factor activity / KEAP1-NFE2L2 pathway / cell-cell signaling / regulation of cell population proliferation / Neddylation / : / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of apoptotic process / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Dipeptidyl-peptidase 3 / Peptidase family M49 / Peptidase family M49 / Angiotensinogen, serpin domain / Angiotensinogen / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Serpin, conserved site / Serpins signature. ...Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Dipeptidyl-peptidase 3 / Peptidase family M49 / Peptidase family M49 / Angiotensinogen, serpin domain / Angiotensinogen / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Angiotensinogen / Dipeptidyl peptidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsKumar, P. / Reisinger, M. / Reithofer, V. / 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 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 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: angiotensin-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6604
Polymers82,5972
Non-polymers632
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-17 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.131, 105.922, 64.846
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1010-

HOH

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Components

#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 angiotensin-II / Serpin A8


Mass: 1048.195 Da / Num. of mol.: 1 / Fragment: UNP residues 34-41 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate dibasic monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2014 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.4→45.33 Å / Num. all: 30464 / Num. obs: 30464 / % possible obs: 97.41 % / Redundancy: 3.6 % / Rsym value: 0.1047 / Net I/σ(I): 9.88
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5771 / Mean I/σ(I) obs: 1.56 / % possible all: 84.18

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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: 2.404→45.33 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1524 5.01 %RANDOM SELECTION
Rwork0.2062 ---
obs0.2083 30446 97.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 2.404→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 2 165 5992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025969
X-RAY DIFFRACTIONf_angle_d0.5778090
X-RAY DIFFRACTIONf_dihedral_angle_d12.5332204
X-RAY DIFFRACTIONf_chiral_restr0.023871
X-RAY DIFFRACTIONf_plane_restr0.0031062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4041-2.48170.411180.31692229X-RAY DIFFRACTION83
2.4817-2.57040.3461330.28142533X-RAY DIFFRACTION94
2.5704-2.67330.35631380.26582619X-RAY DIFFRACTION99
2.6733-2.7950.2961420.24322687X-RAY DIFFRACTION100
2.795-2.94230.2721420.23412713X-RAY DIFFRACTION100
2.9423-3.12660.261420.23432690X-RAY DIFFRACTION100
3.1266-3.36790.25311410.22572679X-RAY DIFFRACTION100
3.3679-3.70670.29651400.23782652X-RAY DIFFRACTION98
3.7067-4.24280.18731400.18162671X-RAY DIFFRACTION98
4.2428-5.34410.20391430.14872713X-RAY DIFFRACTION100
5.3441-45.330.18251450.15172736X-RAY DIFFRACTION99

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