[English] 日本語
Yorodumi- PDB-9b97: Crystal structure of the human PAD2 protein bound to small molecule -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b97 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human PAD2 protein bound to small molecule | ||||||
Components | Protein-arginine deiminase type-2 | ||||||
Keywords | HYDROLASE / Complex | ||||||
Function / homology | Function and homology information negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling / cellular response to leukemia inhibitory factor / nuclear estrogen receptor binding / euchromatin / azurophil granule lumen / chromatin remodeling / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Byrnes, L.J. / Vajdos, F. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2024 Title: Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism. Authors: Byrnes, L.J. / Choi, W.Y. / Balbo, P. / Banker, M.E. / Chang, J. / Chen, S. / Cheng, X. / Cong, Y. / Culp, J. / Di, H. / Griffor, M. / Hall, J. / Meng, X. / Morgan, B. / Mousseau, J.J. / ...Authors: Byrnes, L.J. / Choi, W.Y. / Balbo, P. / Banker, M.E. / Chang, J. / Chen, S. / Cheng, X. / Cong, Y. / Culp, J. / Di, H. / Griffor, M. / Hall, J. / Meng, X. / Morgan, B. / Mousseau, J.J. / Nicki, J. / O'Connell, T. / Ramsey, S. / Shaginian, A. / Shanker, S. / Trujillo, J. / Wan, J. / Vincent, F. / Wright, S.W. / Vajdos, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9b97.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9b97.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9b97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b97_validation.pdf.gz | 688.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9b97_full_validation.pdf.gz | 706.8 KB | Display | |
Data in XML | 9b97_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 9b97_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/9b97 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/9b97 | HTTPS FTP |
-Related structure data
Related structure data | 9b96C 9b98C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 78673.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PAD2, PDI2 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2J8, protein-arginine deiminase |
---|
-Non-polymers , 5 types, 168 molecules
#2: Chemical | ChemComp-MPD / ( | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-A1AJB / ( Mass: 711.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58FN5O3 / Feature type: SUBJECT OF INVESTIGATION | ||||
#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Magnesium acetate, 50mM MES pH5.5, 9-16% 2-methyl 2, 4-pentane diol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→97.289 Å / Num. obs: 25683 / % possible obs: 91.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.95→2.241 Å / Redundancy: 3 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1285 / CC1/2: 0.528 / Rpim(I) all: 0.516 / Rrim(I) all: 0.93 / % possible all: 71.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→97.289 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.326 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.593 / ESU R Free: 0.32 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.275 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→97.289 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|