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- PDB-3smi: Human poly(ADP-ribose) polymerase 14 (Parp14/Artd8) - catalytic d... -

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Basic information

Entry
Database: PDB / ID: 3smi
TitleHuman poly(ADP-ribose) polymerase 14 (Parp14/Artd8) - catalytic domain in complex with a quinazoline inhibitor
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / DIPHTHERIA TOXIN LIKE FOLD / TRANSFERASE / NAD+ / ADP-RIBOSYLATION / TRANSFERASE-TRANSFERASE Inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC
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 / positive regulation of tyrosine phosphorylation of STAT protein / Maturation of nucleoprotein / 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 / positive regulation of tyrosine phosphorylation of STAT protein / Maturation of nucleoprotein / 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 / 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-like, eighth type I KH domain / PARP14, third RRM 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-QDR / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKarlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Nordlund, P. ...Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Nordlund, P. / Nyman, T. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors.
Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. ...Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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)44,8144
Polymers44,2372
Non-polymers5772
Water1,09961
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4072
Polymers22,1191
Non-polymers2881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4072
Polymers22,1191
Non-polymers2881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-4 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.565, 66.417, 145.146
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 / B aggressive lymphoma protein 2


Mass: 22118.590 Da / Num. of mol.: 2 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-QDR / 2-{[(3-amino-1H-1,2,4-triazol-5-yl)sulfanyl]methyl}-8-methylquinazolin-4(3H)-one


Mass: 288.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M NaNO3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 21, 2010 / Details: mirrors and double crystal monochromator
RadiationMonochromator: double crystals Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 16003 / Num. obs: 16003 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 39.21 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.179 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1155 / Rsym value: 0.462 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GOY

3goy


Resolution: 2.4→33.67 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1601 10 %RANDOM
Rwork0.2094 ---
all0.2137 16002 --
obs0.2137 16002 100 %-
Displacement parametersBiso mean: 42.21 Å2
Baniso -1Baniso -2Baniso -3
1--13.1255 Å20 Å20 Å2
2---0.3006 Å20 Å2
3---13.4261 Å2
Refine analyzeLuzzati coordinate error obs: 0.362 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 40 61 2940
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.2772980HARMONIC2
X-RAY DIFFRACTIONt_angle_deg2.134048HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1304SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it2936HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.32
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
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_contact3337SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3082 285 10.01 %
Rwork0.2323 2561 -
all0.2399 2846 -
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)
11.62960.65471.29920.59621.64625.42130.0325-0.26470.08320.1179-0.10680.16660.3812-0.54420.07430.099-0.05390.0004-0.1384-0.0046-0.1548-13.05373.2894-30.1776
22.07020.17231.43514.5266-0.9725.8945-0.00210.09990.1047-0.0482-0.0883-0.0282-0.15910.26240.09040.1499-0.0211-0.007-0.1821-0.0302-0.2262-3.45918.8996-27.6209
30.1272-1.0902-0.73240.3803-0.02750-0.00760.01250.03330.00550.0119-0.0322-0.01580.0347-0.00430.0470.0982-0.00610.0413-0.00680.06867.72610.9033-14.3449
42.7858-0.17911.70783.5996-0.60575.5436-0.021-0.1695-0.01760.1124-0.04110.06830.06670.06980.06210.1515-0.01270.0285-0.16660.0118-0.1834-5.30994.8684-22.3646
51.2179-0.26030.46611.2037-0.67824.13450.08590.0303-0.1452-0.066-0.0490.08260.0699-0.0332-0.0369-0.0292-0.0422-0.0219-0.13510.0196-0.1076-7.5142-2.7934-57.0045
61.03950.21541.01120.62580.36180.1235-0.0094-0.0290.0549-0.0483-0.0130.045-0.0612-0.00380.02240.14150.089-0.02660.01720.00140.0817-11.246913.4987-59.3094
72.56830.1816-0.87453.2843-0.30922.9861-0.0159-0.01850.1787-0.08050.0528-0.0406-0.25870.3514-0.03690.0394-0.06190.0305-0.12140.0361-0.1508-0.52495.8159-60.506
80.9416-0.5786-0.21612.531-1.13711.3169-0.02390.00620.227-0.2014-0.02570.0495-0.21410.09560.04960.1009-0.0294-0.0111-0.08710.0388-0.1084-6.23616.5358-66.8904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1534 - 1615
2X-RAY DIFFRACTION2A1616 - 1669
3X-RAY DIFFRACTION3A1670 - 1681
4X-RAY DIFFRACTION4A1687 - 1720
5X-RAY DIFFRACTION5B1533 - 1614
6X-RAY DIFFRACTION6B1615 - 1630
7X-RAY DIFFRACTION7B1631 - 1680
8X-RAY DIFFRACTION8B1681 - 1720

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