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- PDB-3g0c: Crystal structure of dipeptidyl peptidase IV in complex with a py... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g0c | |||||||||
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Title | Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 1 | |||||||||
![]() | Dipeptidyl peptidase 4![]() | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Kaldor, S.W. / Shi, L. / Skene, R.J. / Aertgeerts, K. / Lee, B. / Jennings, A. ...Zhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Kaldor, S.W. / Shi, L. / Skene, R.J. / Aertgeerts, K. / Lee, B. / Jennings, A. / Xu, R. / Kassel, D. / Webb, D.R. / Gwaltney, S.L. | |||||||||
![]() | ![]() Title: Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV. Authors: Zhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Skene, R.J. / Shi, L. / Lee, B. / Aertgeerts, K. / Jennings, A. / Xu, R. / Kassel, D.B. / Kaldor, S.W. / Navre, M. / Webb, D.R. / Gwaltney, S.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 602.7 KB | Display | ![]() |
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PDB format | ![]() | 492.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3g0bSC ![]() 3g0dC ![]() 3g0gC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 85775.945 Da / Num. of mol.: 4 / Fragment: UNP residues 39-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-RUF / #4: Sugar | ChemComp-NAG / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.56 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion / pH: 7.8 Details: 22.5% PEG MME 200, 0.1M Bicine pH 7.8, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→50 Å / Num. obs: 108584 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Χ2: 1.035 / Net I/σ(I): 12.623 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3G0B Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.817 / SU B: 24.395 / SU ML: 0.255 / SU R Cruickshank DPI: 1.499 / SU Rfree: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.495 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.54 Å2 / Biso mean: 48.26 Å2 / Biso min: 8.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.76 Å / Total num. of bins used: 20
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