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- PDB-9dop: Inhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca... -

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Basic information

Entry
Database: PDB / ID: 9dop
TitleInhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / peptyl arginine deiminase / inhibitor / allosteric / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4903
Polymers74,9661
Non-polymers5242
Water34219
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)143.731, 59.733, 111.149
Angle α, β, γ (deg.)90.000, 122.441, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Protein-arginine deiminase type-4 / HL-60 PAD / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 74965.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PAD4, PADI5, PDI5
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9UM07, protein-arginine deiminase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1BZK / (2R)-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.: 19 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein at 4 mg/mL in buffer 10 mM Tris pH 8.5, 500 mM NaCl, 1 mM DTT, and 1 mM EDTA, and well solution composed of 0.2 M sodium malonate pH 7 and 6% PEG 3350

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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 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→71.26 Å / Num. obs: 14773 / % possible obs: 91.2 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.054 / Rrim(I) all: 0.101 / Net I/σ(I): 10
Reflection shellResolution: 2.441→2.82 Å / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 739 / CC1/2: 0.559 / Rpim(I) all: 0.508 / Rrim(I) all: 0.893 / % possible all: 69.3

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Processing

Software
NameVersionClassification
PHENIXdev_5395refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→71.26 Å / SU ML: 0.3351 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.6547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.293 713 4.83 %
Rwork0.2147 14058 -
obs0.2183 14771 49.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.23 Å2
Refinement stepCycle: LAST / Resolution: 2.44→71.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 34 19 4294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934377
X-RAY DIFFRACTIONf_angle_d1.10035982
X-RAY DIFFRACTIONf_chiral_restr0.055701
X-RAY DIFFRACTIONf_plane_restr0.0084789
X-RAY DIFFRACTIONf_dihedral_angle_d19.34621545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.630.382880.413189X-RAY DIFFRACTION3.37
2.63-2.890.3292490.3371769X-RAY DIFFRACTION13.84
2.89-3.310.36411100.30932310X-RAY DIFFRACTION40.64
3.31-4.170.31052810.2264977X-RAY DIFFRACTION88.28
4.17-71.260.26442650.18945813X-RAY DIFFRACTION99.18
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)
16.399845703743.490731680950.876858463694.966414505041.092594005942.36951564747-0.2254222182680.683596765713-0.496920223421-0.403285780307-0.05337710124720.5318486609220.567465009295-0.318539810980.2001821022330.855548048277-0.01975134601-0.06768465270251.0584587478-0.2178219247470.418893414151246.3911115122.847652318936.31846680271
24.01706828066-0.5351730943291.515263418992.355069140940.9475939207037.789089845170.07281376085840.5219088876640.0238291545195-0.2039412189150.083158953647-0.255930560093-0.2585943231890.560762890198-0.0386806876240.384304757165-0.07275071065370.001494662853840.6129286697770.05158159289240.294305240079266.30005990520.514407570924.5749069634
32.526435919450.3530022751140.2930870283141.18598188840.1671096735825.138472058760.0500944527874-0.4824272394790.1176703185890.210712643949-0.145361080799-0.39867535269-0.1532668478481.071130005490.1993904154970.418620846135-0.0802165125218-0.1380637422640.966528049507-0.03954221818310.471089485335281.69202162519.598364403565.7947700033
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resseq 3:111)3 - 1114 - 98
22(chain A and resseq 112:294)112 - 29499 - 254
33(chain A and resseq 295:663)295 - 663255 - 569

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