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- PDB-9ovq: PAD2 with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 9ovq
TitlePAD2 with an inhibitor
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / Deiminase
Function / homology
Function and homology information


negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / 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 / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / 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
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Cupredoxin
Similarity search - Domain/homology
: / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.175 Å
AuthorsYamaguchi, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Peptidylarginine Deiminase (PAD) Inhibitor Optimization through Displacement of a Trapped Water Molecule
Authors: Schnute, M.E. / Chinigo, G.M. / Futatsugi, K. / Yamaguchi, M. / Bagley, S.W. / Banker, M.E. / Chang, J.S. / Chen, M.Z. / Choi, W.Y. / Corbett, M.S. / Drozda, S.E. / Ebner, D.C. / Garcia- ...Authors: Schnute, M.E. / Chinigo, G.M. / Futatsugi, K. / Yamaguchi, M. / Bagley, S.W. / Banker, M.E. / Chang, J.S. / Chen, M.Z. / Choi, W.Y. / Corbett, M.S. / Drozda, S.E. / Ebner, D.C. / Garcia-Irizarry, C. / Hicklin, R. / Hoy, S. / Jiao, W. / Kortum, S. / Lee, K.L. / Limburg, D.C. / Lovering, F. / Moreno, A. / Mousseau, J.J. / Pan, S. / Parikh, M.D. / Pelker, J.W. / Ramsey, S. / Reilly, U. / Rescourio, G. / Schmitt, D.C. / Simpson, B. / Skrzypek, G.J. / Smaltz, D.J. / Taylor, A.P. / Torella, R. / Trujillo, J.I. / Vajdos, F.F. / Wepy, J.A. / Wright, S.W. / Blakemore, D.C. / Vincent, F. / Clerin, V.M.
History
DepositionMay 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6096
Polymers76,9241
Non-polymers6855
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.936, 51.254, 76.314
Angle α, β, γ (deg.)90, 106.47, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine deiminase type-2 / PAD-H19 / Peptidylarginine deiminase II / Protein-arginine deiminase type II


Mass: 76924.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PAD2, PDI2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical ChemComp-A1CE0 / (2S)-2-amino-2-(1-{(5M)-5-[3,5-dichloro-6-(1-methyl-1H-pyrazol-3-yl)pyridin-2-yl]isoquinolin-1-yl}piperidin-4-yl)-N-methylacetamide


Mass: 524.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27Cl2N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M magnesium acetate, 50 mM MES pH 5.5, and 9-16% 2-methyl 2,4-pentane diol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.175→96.827 Å / Num. obs: 19849 / % possible obs: 99.4 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.175→30.51 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.814 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 947 -RANDOM
Rwork0.2182 ---
obs0.2207 19849 49.9 %-
Displacement parametersBiso mean: 50.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.6208 Å20 Å20.2429 Å2
2---1.6311 Å20 Å2
3---2.2518 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.175→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 40 55 4929
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085054HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956906HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1695SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes883HARMONIC5
X-RAY DIFFRACTIONt_it5027HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion654SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3714SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion19.29
LS refinement shellResolution: 2.175→2.33 Å
RfactorNum. reflection% reflection
Rfree0.295 19 -
Rwork0.2476 --
obs--5.87 %

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