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- PDB-5v7t: crystal structure of PARP14 bound to N-{4-[4-(diphenylmethoxy)pip... -

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Basic information

Entry
Database: PDB / ID: 5v7t
Titlecrystal structure of PARP14 bound to N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine 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 / 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-glutamate ADP-ribosyltransferase activity / 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 / 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-glutamate ADP-ribosyltransferase activity / 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 ...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, 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-91V / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5582
Polymers22,1011
Non-polymers4571
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.301, 83.301, 129.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1949-

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.: 1
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-91V / N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine


Mass: 456.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M Sodium-malonate, pH 7.2-7.8 / PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 277 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.3→72.14 Å / Num. obs: 14218 / % possible obs: 95.5 % / Redundancy: 5.7 % / Net I/σ(I): 24.1
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 752 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.3→72.14 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.396 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29097 567 4.8 %RANDOM
Rwork0.22098 ---
obs0.22139 11306 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.976 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-1.22 Å2-0 Å2
2---2.45 Å2-0 Å2
3---7.93 Å2
Refinement stepCycle: 1 / Resolution: 2.3→72.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 34 67 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191482
X-RAY DIFFRACTIONr_bond_other_d0.0010.021311
X-RAY DIFFRACTIONr_angle_refined_deg0.8891.9472009
X-RAY DIFFRACTIONr_angle_other_deg0.6933007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27824.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62815227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.454157
X-RAY DIFFRACTIONr_chiral_restr0.0580.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
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_it1.6274.388689
X-RAY DIFFRACTIONr_mcbond_other1.6254.388688
X-RAY DIFFRACTIONr_mcangle_it2.5996.572856
X-RAY DIFFRACTIONr_mcangle_other2.5996.573857
X-RAY DIFFRACTIONr_scbond_it1.5524.637792
X-RAY DIFFRACTIONr_scbond_other1.4854.567755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4396.7931104
X-RAY DIFFRACTIONr_long_range_B_refined4.50235.4981676
X-RAY DIFFRACTIONr_long_range_B_other4.42334.8741630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 36 -
Rwork0.355 752 -
obs--88.74 %
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)
13.3675-1.1467-0.55934.5730.02811.84250.1966-0.07790.2137-0.47130.0290.2382-0.08530.0505-0.22560.0956-0.04770.04620.0431-0.06380.1502-6.451421.7152-20.305
29.2945-4.5038-0.99142.6071-0.02570.7118-0.14250.5563-0.84290.276-0.39780.0375-0.23170.11450.54040.2158-0.1113-0.13040.2070.09740.4307-15.781410.5618-27.1526
32.0743-0.39560.38452.587-0.41180.50040.0071-0.11390.03860.09570.11940.0807-0.00840.0806-0.12650.01350.01020.01510.0491-0.05050.4046-6.0519.8392-16.8973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1532 - 1720
2X-RAY DIFFRACTION2A1801
3X-RAY DIFFRACTION3A1901 - 1967

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