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- PDB-6we4: Human PARP14 (ARTD8), catalytic fragment in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 6we4
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with compound 2
ComponentsProtein mono-ADP-ribosyltransferase PARP14
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / PARP14 / ARTD8 / monoPARP / ADP ribosylation / inhibitor complex / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity ...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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / cytoplasm / cytosol
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme ...PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / 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
Similarity search - Domain/homology
Chem-FDR / Chem-TYG / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSwinger, K.S. / Schenkel, L.B. / Kuntz, K.W.
CitationJournal: Cell Chem Biol / Year: 2021
Title: A potent and selective PARP14 inhibitor decreases protumor macrophage gene expression and elicits inflammatory responses in tumor explants.
Authors: Schenkel, L.B. / Molina, J.R. / Swinger, K.K. / Abo, R. / Blackwell, D.J. / Lu, A.Z. / Cheung, A.E. / Church, W.D. / Kunii, K. / Kuplast-Barr, K.G. / Majer, C.R. / Minissale, E. / Mo, J.R. / ...Authors: Schenkel, L.B. / Molina, J.R. / Swinger, K.K. / Abo, R. / Blackwell, D.J. / Lu, A.Z. / Cheung, A.E. / Church, W.D. / Kunii, K. / Kuplast-Barr, K.G. / Majer, C.R. / Minissale, E. / Mo, J.R. / Niepel, M. / Reik, C. / Ren, Y. / Vasbinder, M.M. / Wigle, T.J. / Richon, V.M. / Keilhack, H. / Kuntz, K.W.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP14
B: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,64016
Polymers44,3452
Non-polymers1,29414
Water3,567198
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A: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7518
Polymers22,1731
Non-polymers5797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8888
Polymers22,1731
Non-polymers7167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.107, 67.109, 144.832
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein mono-ADP-ribosyltransferase PARP14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly [ADP-ribose] polymerase 14 / PARP-14


Mass: 22172.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Production host: Escherichia coli (E. coli)
References: UniProt: Q460N5, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 5 types, 212 molecules

#2: Chemical ChemComp-FDR / 2-methyl-3,5,6,7-tetrahydro-4H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one


Mass: 206.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2OS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TYG / 8-methyl-2-{[(pyridin-4-yl)sulfanyl]methyl}quinazolin-4(3H)-one


Mass: 283.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium nitrate, 14% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.6→72.42 Å / Num. obs: 52466 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.026 / Num. unique obs: 3801 / CC1/2: 0.971 / Rpim(I) all: 0.287 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smj

3smj


Resolution: 1.6→72.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.755 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2554 4.9 %RANDOM
Rwork0.2278 ---
obs0.2301 49116 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.39 Å2 / Biso mean: 36.118 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.56 Å20 Å20 Å2
2---0.52 Å20 Å2
3----4.04 Å2
Refinement stepCycle: final / Resolution: 1.6→72.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 106 200 3292
Biso mean--46.8 43.57 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193199
X-RAY DIFFRACTIONr_bond_other_d0.0020.022748
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9494335
X-RAY DIFFRACTIONr_angle_other_deg0.93836393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04424.192167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.476 191 -
Rwork0.459 3538 -
obs--98.05 %

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