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

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Basic information

Entry
Database: PDB / ID: 9dpz
TitlePotent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
Chem-3YZ / : / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 23, 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)75,9523
Polymers74,9661
Non-polymers9862
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.339, 60.421, 113.160
Angle α, β, γ (deg.)90.000, 123.357, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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-A1A9P / (2S)-2-amino-2-{1-[7-(4-bromophenyl)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one


Mass: 511.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H31BrN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3YZ / [(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone


Mass: 474.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate, pH=7, 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 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.406→94.52 Å / Num. obs: 18771 / % possible obs: 69.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 84.62 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 11.8
Reflection shellResolution: 2.41→2.68 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 939 / CC1/2: 0.636 / Rpim(I) all: 0.446 / Rrim(I) all: 1.13 / % possible all: 69.7

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Processing

Software
NameVersionClassification
PHENIXdev_5395refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→47.26 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 926 4.94 %
Rwork0.19 17832 -
obs0.1921 18758 57.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.59 Å2
Refinement stepCycle: LAST / Resolution: 2.41→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 68 27 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014720
X-RAY DIFFRACTIONf_angle_d1.08316442
X-RAY DIFFRACTIONf_chiral_restr0.0573737
X-RAY DIFFRACTIONf_plane_restr0.0086843
X-RAY DIFFRACTIONf_dihedral_angle_d17.71421714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.530.4269150.3567294X-RAY DIFFRACTION6.75
2.53-2.690.3576350.3497667X-RAY DIFFRACTION15.25
2.69-2.90.3452520.34361233X-RAY DIFFRACTION27.75
2.9-3.190.34671380.28432680X-RAY DIFFRACTION60.64
3.19-3.650.29222240.22334014X-RAY DIFFRACTION91.45
3.65-4.60.20142270.1624420X-RAY DIFFRACTION99.94
4.6-47.260.19982350.16274524X-RAY DIFFRACTION99.56
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)
18.203735787663.397551951150.06887980156574.827902832340.3250139629270.2386777282330.06368580158370.59818103666-0.5061476570490.190070589268-0.06621970265740.206071518080.325975609559-0.4088291969170.03014722679320.7831176987970.0718792266322-0.06544110890911.06650677559-0.1393584979180.380058622144-11.074570203614.3118904976-40.4457477735
23.937445848740.136247179582.498302956941.56400208150.8151698247067.70412133365-0.02501166494120.6692208554360.223082307638-0.154939148234-0.0327379602917-0.262834430559-0.1803620605780.792350804126-0.03117723965690.388178315296-0.01726440050550.03274579975030.4984625499280.1004739880180.3386988551639.7116765217933.3242982104-22.5957027464
32.85408932451-0.06591670149280.4049080239381.350016911680.266547566325.828532617650.0332185229982-0.7072868216550.2752293551990.102919579034-0.0491855124309-0.342838642962-0.08634649623041.326404719480.05718319197630.306182311037-0.0436784471776-0.08512016814640.938358552205-0.02298333333380.45827753673824.591763729232.992336794519.5500551144
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 111 )0 - 1111 - 101
22chain 'A' and (resid 112 through 294 )112 - 294102 - 268
33chain 'A' and (resid 295 through 663)295 - 663269 - 596

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