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- PDB-2qky: complex structure of dipeptidyl peptidase IV and a oxadiazolyl ketone -

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Basic information

Entry
Database: PDB / ID: 2qky
Titlecomplex structure of dipeptidyl peptidase IV and a oxadiazolyl ketone
ComponentsDipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
KeywordsHYDROLASE / beta-propeller / dimer / Aminopeptidase / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane
Function / homology
Function and homology information


glucagon processing / 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 / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / 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 / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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-13Z / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKim, K.-H. / Hong, S.Y. / Koo, K.D. / Lee, C.-S. / Kim, G.T. / Han, H.O.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Synthesis, SAR, and X-ray structure of novel potent DPPIV inhibitors: oxadiazolyl ketones.
Authors: Koo, K.D. / Kim, M.J. / Kim, S. / Kim, K.H. / Hong, S.Y. / Hur, G.C. / Yim, H.J. / Kim, G.T. / Han, H.O. / Kwon, O.H. / Kwon, T.S. / Koh, J.S. / Lee, C.S.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
B: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
C: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
D: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,3968
Polymers337,9074
Non-polymers1,4904
Water5,603311
1
A: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
B: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6984
Polymers168,9532
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
D: Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6984
Polymers168,9532
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.178, 106.115, 132.051
Angle α, β, γ (deg.)76.300, 78.620, 80.110
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)


Mass: 84476.648 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI5 / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Chemical
ChemComp-13Z / 2-[(2-{(2S,4S)-2-[(R)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-4-fluoropyrrolidin-1-yl}-2-oxoethyl)amino]-2-methylpropan-1-ol


Mass: 372.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H29FN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24% PEG MME 2K, 0.1M Bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Apr 19, 2004 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 68112 / Num. obs: 64035 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.89 % / Rmerge(I) obs: 0.118 / Χ2: 1.166 / Net I/σ(I): 6.1
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.11 / Num. unique all: 6341 / Χ2: 1.011 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1N1M

1n1m


Resolution: 3.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 4822 7.1 %random
Rwork0.214 ---
all0.214 68112 --
obs0.214 59024 86.7 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 33.698 Å2
Baniso -1Baniso -2Baniso -3
1--4.776 Å22.633 Å2-2.843 Å2
2--3.702 Å2-1.313 Å2
3---1.074 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23860 0 104 311 24275
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION213z.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4carbohydrate.param

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