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- PDB-5nqe: Human PARP14 (ARTD8), catalytic fragment in complex with an N-ary... -

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Basic information

Entry
Database: PDB / ID: 5nqe
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with an N-aryl piperazine inhibitor
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / ADP-ribosylation / Inhibitor complex / Transferase domain
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 / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...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 / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE 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. ...PARP-14, RNA recognition motif 2 / WWE 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. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-94Z / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Schuler, H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14.
Authors: Upton, K. / Meyers, M. / Thorsell, A.G. / Karlberg, T. / Holechek, J. / Lease, R. / Schey, G. / Wolf, E. / Lucente, A. / Schuler, H. / Ferraris, D.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)45,0344
Polymers44,2372
Non-polymers7972
Water30617
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5172
Polymers22,1191
Non-polymers3981
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)22,5172
Polymers22,1191
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.430, 90.360, 80.070
Angle α, β, γ (deg.)90.00, 116.42, 90.00
Int Tables number5
Space group name H-MC121

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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 BL21(DE3) (bacteria) / Variant (production host): R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-94Z / 3-[[4-[4-(4-fluorophenyl)piperazin-1-yl]-4-oxidanylidene-butanoyl]amino]benzamide


Mass: 398.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23FN4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Sodium-malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.71→45.2 Å / Num. all: 97208 / Num. obs: 14476 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 63.32 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.288 / Net I/σ(I): 6.5
Reflection shellResolution: 2.71→2.87 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14938 / CC1/2: 0.641 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1L

4f1l


Resolution: 2.71→45.18 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.681 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.597 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.319
RfactorNum. reflection% reflectionSelection details
Rfree0.258 724 5 %RANDOM
Rwork0.227 ---
obs0.228 14473 99.4 %-
Displacement parametersBiso mean: 40.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.9926 Å20 Å2-1.3639 Å2
2---6.5622 Å20 Å2
3---8.5548 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.71→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 58 17 3005
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013076HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124178HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1354SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3076HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3401SEMIHARMONIC4
LS refinement shellResolution: 2.71→2.93 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3121 148 5.01 %
Rwork0.2798 2808 -
all0.2815 2956 -
obs--98.4 %
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)
11.9494-0.21060.59171.1407-0.06373.1197-0.05630.04040.07190.1055-0.0564-0.0326-0.25650.20570.1127-0.0557-0.0161-0.0093-0.09950.0175-0.1283-0.3191-0.544316.9566
21.7943-0.2434-0.31491.09860.52953.4641-0.0069-0.0623-0.01280.196-0.0607-0.04110.2895-0.26920.0676-0.05-0.0427-0.0248-0.0921-0.0106-0.13062.980833.16516.7188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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