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- PDB-7l9y: Human PARP14 (ARTD8), catalytic fragment in complex with RBN012042 -

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Basic information

Entry
Database: PDB / ID: 7l9y
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with RBN012042
ComponentsProtein mono-ADP-ribosyltransferase PARP14
KeywordsTRANSFERASE/Inhibitor / PARP14 / ARTD8 / monoPARP / ADP ribosylation / inhibitor complex / TRANSFERASE-Inhibitor complex / TRANSFERASE
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. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain ...PARP-14, RNA recognition motif 2 / Parp14 WWE domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / 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
Similarity search - Domain/homology
Chem-XRM / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDorsey, B.W. / Swinger, K.K. / Schenkel, L.B. / Church, W.D. / Perl, N.R. / Vasbinder, M.M. / Wigle, T.J. / Kuntz, K.W.
CitationJournal: Chembiochem / Year: 2021
Title: Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule.
Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B. ...Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B.W. / Niepel, M. / Perl, N.R. / Vasbinder, M.M. / Keilhack, H. / Kuntz, K.W.
History
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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: Protein mono-ADP-ribosyltransferase PARP14
B: Protein mono-ADP-ribosyltransferase PARP14
C: Protein mono-ADP-ribosyltransferase PARP14
D: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,62217
Polymers88,6904
Non-polymers1,93213
Water1,38777
1
A: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6825
Polymers22,1731
Non-polymers5094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7095
Polymers22,1731
Non-polymers5364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5853
Polymers22,1731
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6474
Polymers22,1731
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.650, 92.230, 144.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA1615 - 18018 - 194
21LYSLYSBB1615 - 18018 - 194
12LYSLYSAA1615 - 18018 - 194
22LYSLYSCC1615 - 18018 - 194
13ARGARGAA1615 - 18008 - 193
23ARGARGDD1615 - 18008 - 193
14LYSLYSBB1615 - 18018 - 194
24LYSLYSCC1615 - 18018 - 194
15ARGARGBB1615 - 18008 - 193
25ARGARGDD1615 - 18008 - 193
16ARGARGCC1615 - 18008 - 193
26ARGARGDD1615 - 18008 - 193

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Protein mono-ADP-ribosyltransferase PARP14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly [ADP-ribose] polymerase 14 / PARP-14


Mass: 22172.574 Da / Num. of mol.: 4
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, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-XRM / 7-(cyclopentylamino)-5-fluoro-2-{[(piperidin-4-yl)sulfanyl]methyl}quinazolin-4(3H)-one


Mass: 376.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H25FN4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 26% v/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→46.16 Å / Num. obs: 44437 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 9.3
Reflection shellResolution: 2.25→2.308 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 2 / Num. unique obs: 3210 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smj

3smj


Resolution: 2.25→46.16 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 19.703 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 2273 4.9 %RANDOM
Rwork0.266 ---
obs0.2676 44437 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.28 Å2 / Biso mean: 44.291 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20 Å20 Å2
2--11.34 Å2-0 Å2
3----7.58 Å2
Refinement stepCycle: final / Resolution: 2.25→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 125 77 6259
Biso mean--54.26 31.92 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175697
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6838717
X-RAY DIFFRACTIONr_angle_other_deg1.161.6113117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01922.954369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29415961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9011532
X-RAY DIFFRACTIONr_chiral_restr0.0580.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021614
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62140.07
12B62140.07
21A60190.09
22C60190.09
31A59720.09
32D59720.09
41B60500.09
42C60500.09
51B60080.09
52D60080.09
61C62200.06
62D62200.06
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 174 -
Rwork0.451 3210 -
all-3384 -
obs--99.65 %

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