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- PDB-9b96: Crystal structure of the human PAD2 protein bound to inhibitor -

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Basic information

Entry
Database: PDB / ID: 9b96
TitleCrystal structure of the human PAD2 protein bound to inhibitor
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / Inhibitor / 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
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
: / ACETATE ION / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsByrnes, L.J. / Vajdos, F.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: 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
DepositionApr 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: 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)79,8228
Polymers78,6731
Non-polymers1,1497
Water8,485471
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


  • defined by author&software
  • 160 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)159,64316
Polymers157,3462
Non-polymers2,29714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area9620 Å2
ΔGint-114 kcal/mol
Surface area50780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.260, 50.730, 75.560
Angle α, β, γ (deg.)90.000, 105.077, 90.000
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: 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical ChemComp-A1AJA / 1-({(2P)-1-{(1R)-1-(2-bromophenyl)-3-[5-(methanesulfonamido)-2-methylanilino]-3-oxopropyl}-2-[3-(4-chlorophenoxy)phenyl]-1H-1,3-benzimidazol-6-yl}methyl)-N-methyl-D-prolinamide


Mass: 870.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H42BrClN6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 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

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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 EIGER2 X 9M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→97.659 Å / Num. obs: 61124 / % possible obs: 93.6 % / 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): 13.2
Reflection shellResolution: 1.64→1.801 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3056 / CC1/2: 0.514 / Rpim(I) all: 0.555 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→97.649 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.58 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2114 2970 4.859 %
Rwork0.1721 58153 -
all0.174 --
obs-61123 67.133 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.016 Å2
2--0.039 Å20 Å2
3----0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.64→97.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 69 471 5578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164856
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6357149
X-RAY DIFFRACTIONr_angle_other_deg0.5141.56711330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5635642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.3611031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6210909
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.58810231
X-RAY DIFFRACTIONr_chiral_restr0.0770.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021056
X-RAY DIFFRACTIONr_nbd_refined0.2180.2868
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24591
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2455
X-RAY DIFFRACTIONr_metal_ion_refined0.3190.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.240
X-RAY DIFFRACTIONr_nbd_other0.2040.2143
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1290.22
X-RAY DIFFRACTIONr_mcbond_it2.5972.6042552
X-RAY DIFFRACTIONr_mcbond_other2.5972.6022550
X-RAY DIFFRACTIONr_mcangle_it3.9763.8773181
X-RAY DIFFRACTIONr_mcangle_other3.9763.8793182
X-RAY DIFFRACTIONr_scbond_it3.5783.0922734
X-RAY DIFFRACTIONr_scbond_other3.5773.0932735
X-RAY DIFFRACTIONr_scangle_it5.5674.4413963
X-RAY DIFFRACTIONr_scangle_other5.5664.4423964
X-RAY DIFFRACTIONr_lrange_it8.10944.0995900
X-RAY DIFFRACTIONr_lrange_other8.01442.0095755
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.64-1.6820.28280.2982140.29867130.9410.9493.3070.288
1.682-1.7290.373320.3178510.31965000.9230.93713.58460.307
1.729-1.7790.328670.29812340.29963240.9320.94120.57240.284
1.779-1.8330.28960.2716640.2761570.9540.95428.58540.244
1.833-1.8940.2671250.24823080.24960000.9570.96140.550.213
1.894-1.960.2691620.24332090.24457690.9470.96158.4330.205
1.96-2.0340.2582330.23440760.23655800.9560.96377.22220.187
2.034-2.1170.2552230.21945390.22154220.9550.96787.82740.178
2.117-2.2110.2382320.20746570.20951410.9630.97195.09820.168
2.211-2.3190.2252530.18946510.19149220.9670.97899.63430.154
2.319-2.4440.2122340.1844460.18146890.9740.9899.80810.148
2.444-2.5920.2342170.16742310.1744680.9670.98399.55240.139
2.592-2.7710.2211990.16539530.16741710.9710.98499.54450.141
2.771-2.9930.1931900.15736980.15939190.9770.98599.2090.141
2.993-3.2780.1831590.1634190.16135990.9790.98599.41650.15
3.278-3.6650.2021770.15830540.1632630.9750.98699.01930.157
3.665-4.2310.1731250.14127420.14229100.9830.98898.52230.148
4.231-5.1790.1571030.12523390.12624580.9880.99199.34910.14
5.179-7.3140.23800.17618370.17819370.9680.98598.96750.195
7.314-97.6490.232550.17910310.18211060.9460.97198.19170.226

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