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- PDB-9dol: Potent inhibition of the protein arginine deiminases (PAD1-4) by ... -

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Basic information

Entry
Database: PDB / ID: 9dol
TitlePotent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / peptylarginine deiminase / inhibitor / allosteric
Function / homology
Function and homology information


negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / histone H4R3 arginine deiminase activity / histone H1R54 arginine deiminase activity ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / histone H4R3 arginine deiminase activity / histone H1R54 arginine deiminase activity / histone H2AR3 arginine deiminase activity / 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: 1.77 Å
AuthorsLiu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Inhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca 2+ dependent allosteric binding site.
Authors: Dakin, L.A. / Xing, L. / Hall, J. / Ding, W. / Vajdos, F.F. / Pelker, J.W. / Ramsey, S. / Balbo, P. / Sahasrabudhe, P.V. / Banker, M.E. / Choi, W.Y. / Wright, S.W. / Chang, J.S. / Curto, J.M. ...Authors: Dakin, L.A. / Xing, L. / Hall, J. / Ding, W. / Vajdos, F.F. / Pelker, J.W. / Ramsey, S. / Balbo, P. / Sahasrabudhe, P.V. / Banker, M.E. / Choi, W.Y. / Wright, S.W. / Chang, J.S. / Curto, J.M. / Davoren, J.E. / Drozda, S.E. / Fennell, K.F. / Futatsugi, K. / Kortum, S. / Lee, K.L. / Liu, S. / Lovering, F. / Nicki, J.A. / Trujillo, J.I. / Vincent, F. / Schnute, M.E.
History
DepositionSep 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,3186
Polymers78,6731
Non-polymers6455
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.127, 51.051, 76.208
Angle α, β, γ (deg.)90.00, 106.28, 90.00
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: Insect expression vector pBlueBacmsGCA1C239A-C244A (others)
References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#3: Chemical ChemComp-A1A8O / (2S)-2-amino-2-{1-[(5M)-5-(3,5-dichloropyridin-2-yl)isoquinolin-1-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one


Mass: 484.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27Cl2N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein at 8 mg/mL in buffer 20 mM Tris pH 7.5, 10% glycerol, 500 mM NaCl, 0.5 mM TCEP, and 1 mM EDTA, and well solution composed of 0.1 M magnesium acetate, 50 mM MES pH 5.5, and 9-16% 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 EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→96.6 Å / Num. obs: 40310 / % possible obs: 92.7 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.6
Reflection shellResolution: 1.77→2.02 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2014 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→96.53 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1899 4.71 %
Rwork0.1849 --
obs0.1869 40305 55.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→96.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 37 378 5525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035337
X-RAY DIFFRACTIONf_angle_d0.5977265
X-RAY DIFFRACTIONf_dihedral_angle_d12.961974
X-RAY DIFFRACTIONf_chiral_restr0.045806
X-RAY DIFFRACTIONf_plane_restr0.004957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.297960.420653X-RAY DIFFRACTION1
1.82-1.860.314660.3469195X-RAY DIFFRACTION4
1.87-1.920.3668310.309440X-RAY DIFFRACTION9
1.92-1.980.2886270.2829708X-RAY DIFFRACTION14
1.98-2.050.3017540.26781079X-RAY DIFFRACTION22
2.05-2.130.2935810.27081573X-RAY DIFFRACTION32
2.14-2.230.30171130.26332371X-RAY DIFFRACTION48
2.23-2.350.27731570.26383336X-RAY DIFFRACTION68
2.35-2.50.26361960.25284135X-RAY DIFFRACTION84
2.5-2.690.26122470.23334867X-RAY DIFFRACTION98
2.69-2.960.27842530.20994899X-RAY DIFFRACTION100
2.96-3.390.24282520.17754918X-RAY DIFFRACTION99
3.39-4.270.18982200.14374934X-RAY DIFFRACTION98
4.27-96.530.19252560.15984898X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6606-2.53871.5683.372-1.77576.47650.19740.28090.2712-0.2657-0.09420.1393-0.43710.0082-0.10480.20970.0438-0.0070.2384-0.12710.3687338.303710.785367.5758
23.7254-0.78751.52850.944-0.18991.5449-0.0745-0.8374-0.22540.07670.06950.14650.074-0.41570.00920.1882-0.01770.08810.3550.04240.2387357.0611-3.0987.1952
34.0934-0.09532.35840.81150.21162.36040.1182-0.7299-0.30920.30080.0756-0.16330.3098-0.0994-0.21720.29250.01410.04790.38440.06930.1931390.95-6.8661101.4121
43.9885-0.10130.76011.11090.15291.9706-0.0566-0.2082-0.18360.22460.0699-0.15840.10450.10540.01130.14840.03510.00140.10490.03880.1322406.6226-6.183890.8916
55.12020.51760.75971.04720.22361.2757-0.0411-0.7927-0.26010.39820.0611-0.21030.01350.0679-0.0270.32090.0195-0.02190.35920.02030.2301404.893-3.6712100.7721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 359 )
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 601 )
5X-RAY DIFFRACTION5chain 'A' and (resid 602 through 668 )

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