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- PDB-6fzm: Human PARP14 (ARTD8), catalytic fragment in complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 6fzm
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with inhibitor ITK6
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / ADP-RIBOSYLATION / INHIBITOR COMPLEX / TRANSFERASE DOMAIN
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. ...PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-EE5 / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Kirby, I.T. / Sreenivasan, R. / Cohen, M.S. / Schuler, H.
CitationJournal: Cell Chem Biol / Year: 2018
Title: A Potent and Selective PARP11 Inhibitor Suggests Coupling between Cellular Localization and Catalytic Activity.
Authors: Kirby, I.T. / Kojic, A. / Arnold, M.R. / Thorsell, A.G. / Karlberg, T. / Vermehren-Schmaedick, A. / Sreenivasan, R. / Schultz, C. / Schuler, H. / Cohen, M.S.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 14
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9664
Polymers44,2372
Non-polymers7292
Water27015
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4832
Polymers22,1191
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4832
Polymers22,1191
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.885, 83.885, 204.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Poly [ADP-ribose] polymerase 14 / PARP-14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2


Mass: 22118.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-EE5 / 4-[(8-methyl-4-oxidanylidene-7-prop-1-ynyl-3~{H}-quinazolin-2-yl)methylsulfanyl]benzoic acid


Mass: 364.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% Poly(ethylene glycol) 3350, 0.2M sodium nitrate and 0.1M Bis-Tris-Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.67→49.76 Å / Num. obs: 12549 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 34.8 % / Biso Wilson estimate: 66.3 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.446 / Rrim(I) all: 0.453 / Net I/σ(I): 10.6
Reflection shellResolution: 2.67→2.83 Å / Redundancy: 30.5 % / Rmerge(I) obs: 1.913 / Mean I/σ(I) obs: 2 / Num. unique obs: 1739 / CC1/2: 0.769 / Rrim(I) all: 1.945 / % possible all: 86.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1L

4f1l


Resolution: 2.67→49.76 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.853 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 4.24 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389 / SU Rfree Cruickshank DPI: 0.387
RfactorNum. reflection% reflectionSelection details
Rfree0.289 626 5.01 %RANDOM
Rwork0.235 ---
obs0.237 12505 97.5 %-
Displacement parametersBiso mean: 51.93 Å2
Baniso -1Baniso -2Baniso -3
1-10.8498 Å20 Å20 Å2
2--10.8498 Å20 Å2
3----21.6996 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: 1 / Resolution: 2.67→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 52 15 3109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013186HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074333HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1399SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it3186HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion394SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3449SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 134 5.01 %
Rwork0.268 2542 -
all0.273 2676 -
obs--90.33 %
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)
12.98910.53250.08581.4789-0.50051.92430.0509-0.102-0.0592-0.01980.04010.0757-0.1472-0.0963-0.091-0.19380.007-0.0028-0.21710.00560.181-12.4345-15.6109-11.2955
24.4376-0.7760.14062.2167-0.29681.5229-0.0313-0.18960.1285-0.01950.0025-0.07570.04860.10670.0288-0.2154-0.00650.0202-0.21940.03860.164115.6053-35.0427-11.5241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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