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- PDB-2gbg: rat DPP-IV with alkynyl cyanopyrrolidine #2 -

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Basic information

Entry
Database: PDB / ID: 2gbg
Titlerat DPP-IV with alkynyl cyanopyrrolidine #2
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE / serine peptidase beta propeller
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-1AD / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLongenecker, K.L. / Jakob, C.G. / Fry, E.H. / Wilk, S.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors.
Authors: Longenecker, K.L. / Stewart, K.D. / Madar, D.J. / Jakob, C.G. / Fry, E.H. / Wilk, S. / Lin, C.W. / Ballaron, S.J. / Stashko, M.A. / Lubben, T.H. / Yong, H. / Pireh, D. / Pei, Z. / Basha, F. ...Authors: Longenecker, K.L. / Stewart, K.D. / Madar, D.J. / Jakob, C.G. / Fry, E.H. / Wilk, S. / Lin, C.W. / Ballaron, S.J. / Stashko, M.A. / Lubben, T.H. / Yong, H. / Pireh, D. / Pei, Z. / Basha, F. / Wiedeman, P.E. / Von Geldern, T.W. / Trevillyan, J.M. / Stoll, V.S.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: 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
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

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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)169,0354
Polymers168,6752
Non-polymers3592
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-32 kcal/mol
Surface area56670 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)507,10412
Polymers506,0256
Non-polymers1,0786
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 area22360 Å2
ΔGint-145 kcal/mol
Surface area162750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.500, 207.500, 207.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Detailsdimer of asymmetric unit is thought to be biologically relevant

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Components

#1: Protein Dipeptidyl peptidase 4 / Dipeptidyl peptidase-4


Mass: 84337.578 Da / Num. of mol.: 2
Fragment: Dipeptidyl Peptidase 4 Soluble Form (Residues 38-767)
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-1AD / (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-PROP-1-YN-1-YLPYRROLIDIN-1-YL]-1-CYCLOPENTYL-2-OXOETHANAMINE


Mass: 263.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O

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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: 4.41 Å3/Da / Density % sol: 72.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.8 M ammonium sulfate and 100mM sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / 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: 59362 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.106 / Χ2: 1.097 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
3-3.1199.46.40.68858710.817
3.11-3.2399.66.70.4658890.867
3.23-3.3899.76.80.33758940.882
3.38-3.5699.770.23159100.953
3.56-3.7899.97.10.16159661.009
3.78-4.0799.97.20.11859641.074
4.07-4.4899.87.30.08259041.167
4.48-5.1399.57.40.06559531.252
5.13-6.4699.27.50.06259991.156
6.46-5097.27.40.04560121.676

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 2997 5 %
Rwork0.235 --
obs-59077 99.4 %
Displacement parametersBiso mean: 57.058 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 24 0 11864
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_repADD.param
X-RAY DIFFRACTION2add.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.param

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