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- PDB-4py4: Crystal structure of human poly(ADP-ribose) polymerase 14, cataly... -

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Basic information

Entry
Database: PDB / ID: 4py4
TitleCrystal structure of human poly(ADP-ribose) polymerase 14, catalytic domain in complex with an inhibitor XL2
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTransferase/Transferase Inhibitor / Rossmann Fold / catalyze the post-translational modification of proteins / using b-NAD+ / 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 / 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 / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / 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 / nucleus / membrane / 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, 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-XL2 / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsLi, J. / Xu, Y.
CitationJournal: Tetrahedron / Year: 2017
Title: Palladium-catalyzed N-arylation of 2-aminobenzothiazole-4-carboxylates/carboxamides: facile synthesis of PARP14 inhibitors
Authors: Wang, P. / Li, J. / Jiang, X. / Liu, Z. / Ye, N. / Xu, Y. / Yang, G. / Xu, Y. / Zhang, A.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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)44,0254
Polymers43,3082
Non-polymers7172
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-3 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.580, 66.910, 144.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 21654.033 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 1613-1801
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-XL2 / 2-({4-[(1R)-1-(dimethylamino)ethyl]phenyl}amino)-6-fluoro-1,3-benzothiazole-4-carboxamide


Mass: 358.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19FN4OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M Sodium-malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 18644 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.73
Reflection shellResolution: 2.76→2.83 Å / % possible all: 91.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1L

4f1l


Resolution: 2.76→39.123 Å / FOM work R set: 0.8182 / SU ML: 0.3 / σ(F): 1.11 / Phase error: 25.07 / Stereochemistry target values: MLHL
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.257 562 3.02 %
Rwork0.2018 --
obs0.2035 18632 86.66 %
all-18644 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 25.08 Å2 / Biso min: 5.98 Å2
Refinement stepCycle: LAST / Resolution: 2.76→39.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 50 8 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092942
X-RAY DIFFRACTIONf_angle_d1.1393996
X-RAY DIFFRACTIONf_chiral_restr0.077408
X-RAY DIFFRACTIONf_plane_restr0.005523
X-RAY DIFFRACTIONf_dihedral_angle_d14.7051062
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7601-3.03780.30471440.2534644478889
3.0378-3.47710.28461450.22044559470487
3.4771-4.37990.26661350.18534478461386
4.3799-39.12720.21581380.1864389452784

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