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- PDB-5v7w: Crystal structure of human PARP14 bound to 2-{[(1-methylpiperidin... -

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Basic information

Entry
Database: PDB / ID: 5v7w
TitleCrystal structure of human PARP14 bound to 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one inhibitor
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / HUMAN PARP14 / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / : / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / 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 / : / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / 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 / : / : / : / : / : / : / : / : / Parp14 WWE domain ...PARP-14, RNA recognition motif 2 / : / : / : / : / : / : / : / : / Parp14 WWE domain / PARP14, first type I KH 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 / : / PAR14-like, first RRM domain / : / PARP14-like, eighth type I KH domain / PARP14, third RRM 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-91J / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
Authorssaikatendu, k.s. / Hirozane, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation.
Authors: Yoneyama-Hirozane, M. / Matsumoto, S.I. / Toyoda, Y. / Saikatendu, K.S. / Zama, Y. / Yonemori, K. / Oonishi, M. / Ishii, T. / Kawamoto, T.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,8684
Polymers44,2032
Non-polymers6652
Water2,378132
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4342
Polymers22,1011
Non-polymers3321
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)22,4342
Polymers22,1011
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.049, 144.907, 83.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2064-

HOH

21B-2035-

HOH

31B-2068-

HOH

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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: 22101.496 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, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-91J / 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one


Mass: 332.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H24N4OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M Sodium-malonate, pH 7.2-7.8

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Data collection

DiffractionMean temperature: 277 K / Ambient temp details: CRYO
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2398 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.6→72.45 Å / Num. obs: 14247 / % possible obs: 99.88 % / Redundancy: 3.7 % / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.65→72.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 35.708 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.329 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26595 758 5.1 %RANDOM
Rwork0.20351 ---
obs0.20678 14247 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.378 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å2-0 Å2
2---4.36 Å20 Å2
3---1.94 Å2
Refinement stepCycle: 1 / Resolution: 2.65→72.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 46 132 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.944019
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21924.312160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4941515
X-RAY DIFFRACTIONr_chiral_restr0.0650.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3961.5461382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8362.311717
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6651.7371572
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.56313.6714558
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.31332954
X-RAY DIFFRACTIONr_sphericity_free42.093554
X-RAY DIFFRACTIONr_sphericity_bonded9.0452947
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 62 -
Rwork0.332 1022 -
obs--99.27 %
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)
12.2185-0.40960.19264.181-0.43251.0944-0.0113-0.0805-0.15160.350.03650.5770.0511-0.1202-0.02520.368-0.01370.0640.2715-0.03550.2834-25.99717.944918.4523
22.52770.2346-0.47233.3688-0.23351.51870.00260.09370.1152-0.22460.0550.1375-0.0692-0.0543-0.05760.35030.0068-0.02070.2843-0.0160.1843-25.9951.083222.46
30.1169-0.09260.06390.5540.07920.38160.0307-0.0127-0.0196-0.0432-0.02520.0153-0.01380.0136-0.00550.0114-0.01480.00310.18830.01240.1713-24.371434.900821.0517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1614 - 1801
2X-RAY DIFFRACTION2B1612 - 1801
3X-RAY DIFFRACTION3A2001 - 2064
4X-RAY DIFFRACTION3B2001 - 2068

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