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- PDB-6g0w: Human PARP14 (ARTD8), catalytic fragment in complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 6g0w
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with inhibitor MCD72
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / ADP-RIBOSYLATION / INHIBITOR COMPLEX / TRANSFERASE DOMAIN
Function / homology
Function and homology information


negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / Nicotinamide salvage / Maturation of nucleoprotein / NAD+-protein-glutamate ADP-ribosyltransferase activity / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity ...negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / Nicotinamide salvage / Maturation of nucleoprotein / NAD+-protein-glutamate ADP-ribosyltransferase activity / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / : / Parp14 WWE domain / PARP14, first type I KH domain / PAR14-like, first RRM domain / PARP14, second RRM domain / PARP14, second type I KH domain / PARP14, third type I KH domain / PARP14, fourth type I KH domain / PARP14, fifth type I KH domain ...PARP-14, RNA recognition motif 2 / : / Parp14 WWE domain / PARP14, first type I KH domain / PAR14-like, first RRM domain / PARP14, second RRM domain / PARP14, second type I KH domain / PARP14, third type I KH domain / PARP14, fourth type I KH domain / PARP14, fifth type I KH domain / PARP14, sixth type I KH domain / PARP14, third RRM domain / PARP14-like, eighth type I KH 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-EGW / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Holechek, J. / Lease, R. / Ferraris, D. / Schuler, H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14.
Authors: Holechek, J. / Lease, R. / Thorsell, A.G. / Karlberg, T. / McCadden, C. / Grant, R. / Keen, A. / Callahan, E. / Schuler, H. / Ferraris, D.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)45,0744
Polymers44,2372
Non-polymers8372
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-2 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.314, 83.314, 255.495
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1901-

EGW

21B-1901-

EGW

31B-1901-

EGW

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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-EGW / 4-[3-[4-(4-fluorophenyl)piperidin-1-yl]carbonylphenoxy]benzamide


Mass: 418.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23FN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG6000, 0.2M magnesium chloride, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→47.83 Å / Num. obs: 23094 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.3 % / Biso Wilson estimate: 44.05 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.208 / Net I/σ(I): 13.2
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 25.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3594 / CC1/2: 0.854 / Rrim(I) all: 1.396 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1L

4f1l


Resolution: 2.34→47.826 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.18
RfactorNum. reflection% reflection
Rfree0.2746 1155 5 %
Rwork0.2236 --
obs0.2262 23086 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.34→47.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 62 21 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093125
X-RAY DIFFRACTIONf_angle_d1.1114243
X-RAY DIFFRACTIONf_dihedral_angle_d11.1041875
X-RAY DIFFRACTIONf_chiral_restr0.087434
X-RAY DIFFRACTIONf_plane_restr0.007605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3373-2.44370.38061390.31772648X-RAY DIFFRACTION98
2.4437-2.57250.34161400.29472654X-RAY DIFFRACTION100
2.5725-2.73370.3111410.25172674X-RAY DIFFRACTION100
2.7337-2.94480.32311420.23822708X-RAY DIFFRACTION100
2.9448-3.2410.31541430.23352716X-RAY DIFFRACTION100
3.241-3.70990.26681450.21042738X-RAY DIFFRACTION100
3.7099-4.67340.23441470.1892798X-RAY DIFFRACTION100
4.6734-47.83580.24961580.21692995X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.5565 Å / Origin y: -11.7597 Å / Origin z: -21.3022 Å
111213212223313233
T0.264 Å20.0277 Å20.001 Å2-0.2926 Å20.037 Å2--0.2397 Å2
L0.9673 °20.156 °20.203 °2-0.8593 °2-0.1611 °2--0.2905 °2
S0.0419 Å °-0.0639 Å °-0.0826 Å °-0.078 Å °-0.0121 Å °0.036 Å °0.0192 Å °0.0146 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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