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- PDB-2oae: Crystal structure of rat dipeptidyl peptidase (DPPIV) with thiazo... -

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Basic information

Entry
Database: PDB / ID: 2oae
TitleCrystal structure of rat dipeptidyl peptidase (DPPIV) with thiazole-based peptide mimetic #31
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE / serine-peptidase / inhibitor complex
Function / homology
Function and homology information


B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus ...B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / positive regulation of natural killer cell mediated immunity / dipeptidyl-peptidase activity / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / collagen binding / T cell costimulation / serine-type peptidase activity / T cell activation / peptide binding / protein catabolic process / virus receptor activity / lamellipodium / protease binding / response to hypoxia / cell adhesion / membrane raft / apical plasma membrane / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain ...Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AIL / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLongenecker, K.L. / Shuai, Q. / Patel, J. / Wiedeman, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Pyrrolidine-constrained phenethylamines: The design of potent, selective, and pharmacologically efficacious dipeptidyl peptidase IV (DPP4) inhibitors from a lead-like screening hit.
Authors: Backes, B.J. / Longenecker, K. / Hamilton, G.L. / Stewart, K. / Lai, C. / Kopecka, H. / von Geldern, T.W. / Madar, D.J. / Pei, Z. / Lubben, T.H. / Zinker, B.A. / Tian, Z. / Ballaron, S.J. / ...Authors: Backes, B.J. / Longenecker, K. / Hamilton, G.L. / Stewart, K. / Lai, C. / Kopecka, H. / von Geldern, T.W. / Madar, D.J. / Pei, Z. / Lubben, T.H. / Zinker, B.A. / Tian, Z. / Ballaron, S.J. / Stashko, M.A. / Mika, A.K. / Beno, D.W. / Kempf-Grote, A.J. / Black-Schaefer, C. / Sham, H.L. / Trevillyan, J.M.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,0984
Polymers168,6752
Non-polymers4232
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-36 kcal/mol
Surface area56370 Å2
MethodPISA
2
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules

A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules

A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,29312
Polymers506,0256
Non-polymers1,2686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area22550 Å2
ΔGint-153 kcal/mol
Surface area161930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.349, 208.349, 208.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
DetailsThe dimer of the asymmetric unit is thought to be biologically relevant

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Components

#1: Protein Dipeptidyl peptidase 4 / Dipeptidyl peptidase-4 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / GP110 glycoprotein / Bile ...Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / GP110 glycoprotein / Bile canaliculus domain-specific membrane glycoprotein


Mass: 84337.578 Da / Num. of mol.: 2 / Fragment: Soluble form: Residues 37-767 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P14740, dipeptidyl-peptidase IV
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AIL / N-{[(3S,5S)-5-(1,3-THIAZOLIDIN-3-YLCARBONYL)PYRROLIDIN-3-YL]METHYL}-1,3-THIAZOLE-4-CARBOXAMIDE


Mass: 326.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O2S2

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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

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 60215 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.14 / Χ2: 1.138 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.115.90.53360010.28999.9
3.11-3.236.20.3859170.35499.9
3.23-3.386.40.30859800.425100
3.38-3.566.60.25959840.622100
3.56-3.786.90.19359920.774100
3.78-4.077.10.16259681.073100
4.07-4.487.30.12660221.446100
4.48-5.137.60.11160391.796100
5.13-6.467.70.10460751.614100
6.46-507.10.07362372.3899.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / FOM work R set: 0.756 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.28 3039 5.1 %
Rwork0.249 --
obs-59968 99.7 %
Displacement parametersBiso mean: 49.497 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 26 0 11866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3-3.020.428490.40910071056
3.02-3.040.449460.45710971143
3.04-3.060.523620.42311471209
3.06-3.080.466660.40911261192
3.08-3.110.441540.38511771231
3.11-3.130.374640.34110841148
3.13-3.150.433620.36511591221
3.15-3.180.397680.35711061174
3.18-3.20.377740.34511371211
3.2-3.230.34510.3311191170
3.23-3.260.356700.32411411211
3.26-3.290.325560.34111211177
3.29-3.320.436510.34511451196
3.32-3.350.348520.31611201172
3.35-3.380.299650.33911371202
3.38-3.410.458550.32311621217
3.41-3.440.366560.29911111167
3.44-3.480.315630.31311641227
3.48-3.520.33490.29911221171
3.52-3.550.408620.29911341196
3.55-3.590.343640.29211751239
3.59-3.640.303440.26811251169
3.64-3.680.293610.26911401201
3.68-3.730.299800.2611181198
3.73-3.780.264550.25711171172
3.78-3.830.254730.22811301203
3.83-3.880.274490.2311871236
3.88-3.940.292600.23410951155
3.94-40.278680.22911451213
4-4.060.224520.21911281180
4.06-4.130.249650.21411341199
4.13-4.210.233610.21211431204
4.21-4.290.247750.19911371212
4.29-4.380.244520.1911261178
4.38-4.470.215600.18311741234
4.47-4.570.202600.18611281188
4.57-4.690.193540.17811431197
4.69-4.810.223680.17911561224
4.81-4.950.189710.18111201191
4.95-5.110.198690.18511601229
5.11-5.290.221710.19911161187
5.29-5.490.208600.19511621222
5.49-5.740.235540.20611521206
5.74-6.030.244550.21211701225
6.03-6.40.273550.23211601215
6.4-6.870.216590.23511561215
6.87-7.530.313830.23711451228
7.53-8.550.289570.22411641221
8.55-10.50.251570.23212031260
10.5-200.266720.26612041276
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_repADD.param
X-RAY DIFFRACTION2lig.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.param

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