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- PDB-5lyh: Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor H10 -

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Basic information

Entry
Database: PDB / ID: 5lyh
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with inhibitor H10
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+-protein poly-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+-protein poly-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 / Parp14 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-14, RNA recognition motif 2 / Parp14 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-7B8 / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Schuler, H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Small Molecule Microarray Based Discovery of PARP14 Inhibitors.
Authors: Peng, B. / Thorsell, A.G. / Karlberg, T. / Schuler, H. / Yao, S.Q.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)45,3524
Polymers44,2372
Non-polymers1,1152
Water34219
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6762
Polymers22,1191
Non-polymers5581
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)22,6762
Polymers22,1191
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.032, 83.032, 122.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1613 - 1801 / Label seq-ID: 5 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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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-7B8 / 3-[2-[4-[2-[[4-[(3-aminocarbonylphenyl)amino]-4-oxidanylidene-butanoyl]amino]ethyl]-1,2,3-triazol-1-yl]ethylsulfamoyl]benzoic acid


Mass: 557.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N7O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 22.5% PEG3350, 0.225M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97999 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.658
11-h,-k,l20.342
ReflectionResolution: 2.17→46.5 Å / Num. obs: 26408 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14
Reflection shellResolution: 2.17→2.3 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2 / CC1/2: 0.754 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1L

4f1l


Resolution: 2.17→46.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.206 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21783 2004 7.6 %RANDOM
Rwork0.19535 ---
obs0.19703 24403 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.287 Å2
Baniso -1Baniso -2Baniso -3
1--31.74 Å2-0 Å2-0 Å2
2---31.74 Å2-0 Å2
3---63.49 Å2
Refinement stepCycle: 1 / Resolution: 2.17→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 78 19 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023161
X-RAY DIFFRACTIONr_bond_other_d0.0060.022833
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9484297
X-RAY DIFFRACTIONr_angle_other_deg1.2713.0076498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7535365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27924.226168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7821516
X-RAY DIFFRACTIONr_chiral_restr0.10.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213664
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02824
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_it5.1625.9441466
X-RAY DIFFRACTIONr_mcbond_other5.1575.9431465
X-RAY DIFFRACTIONr_mcangle_it7.3778.9021826
X-RAY DIFFRACTIONr_mcangle_other7.3758.9031827
X-RAY DIFFRACTIONr_scbond_it4.9456.3661692
X-RAY DIFFRACTIONr_scbond_other4.9446.3641693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3419.4332469
X-RAY DIFFRACTIONr_long_range_B_refined10.62847.3683404
X-RAY DIFFRACTIONr_long_range_B_other10.62747.3653404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20500 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.166→2.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 138 -
Rwork0.338 1711 -
obs--95.85 %

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