+Open data
-Basic information
Entry | Database: PDB / ID: 7svn | ||||||
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Title | DPP9 IN COMPLEX WITH LIGAND ICeD-1 | ||||||
Components | Dipeptidyl peptidase 9 | ||||||
Keywords | HYDROLASE / DIPEPTIDYL PEPTIDASE | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Lammens, A. / Hollenstein, K. / Klein, D.J. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells. Authors: Moore, K.P. / Schwaid, A.G. / Tudor, M. / Park, S. / Beshore, D.C. / Converso, A. / Shipe, W.D. / Anand, R. / Lan, P. / Moningka, R. / Rothman, D.M. / Sun, W. / Chi, A. / Cornella-Taracido, ...Authors: Moore, K.P. / Schwaid, A.G. / Tudor, M. / Park, S. / Beshore, D.C. / Converso, A. / Shipe, W.D. / Anand, R. / Lan, P. / Moningka, R. / Rothman, D.M. / Sun, W. / Chi, A. / Cornella-Taracido, I. / Adam, G.C. / Bahnck-Teets, C. / Carroll, S.S. / Fay, J.F. / Goh, S.L. / Lusen, J. / Quan, S. / Rodriguez, S. / Xu, M. / Andrews, C.L. / Song, C. / Filzen, T. / Li, J. / Hollenstein, K. / Klein, D.J. / Lammens, A. / Lim, U.M. / Fang, Z. / McHale, C. / Li, Y. / Lu, M. / Diamond, T.L. / Howell, B.J. / Zuck, P. / Balibar, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7svn.cif.gz | 685.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7svn.ent.gz | 557.4 KB | Display | PDB format |
PDBx/mmJSON format | 7svn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7svn ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7svn | HTTPS FTP |
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-Related structure data
Related structure data | 7svlC 7svmC 7svoC 6eoqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 99213.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV #2: Chemical | ChemComp-CW8 / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 10% PEG 8000 25% glycerol 0.16 M calcium acetate 0.08 M cacodilate pH 6.25 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→157.52 Å / Num. obs: 103766 / % possible obs: 94.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 1.92 |
Reflection shell | Resolution: 2.78→3.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.593 / Num. unique obs: 23973 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EOQ Resolution: 2.78→157.52 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.824 / SU B: 23.704 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 229.61 Å2 / Biso mean: 42.485 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.78→157.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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