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- PDB-5lx6: Human PARP10 (ARTD10), catalytic fragment in complex with PARP in... -

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Basic information

Entry
Database: PDB / ID: 5lx6
TitleHuman PARP10 (ARTD10), catalytic fragment in complex with PARP inhibitor Veliparib
ComponentsPoly [ADP-ribose] polymerase 10
KeywordsTRANSFERASE / Transferase domain / ADP-ribosylation / PARP inhibitor
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / : / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation ...negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / : / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of NF-kappaB transcription factor activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / translesion synthesis / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / nucleolus / Golgi apparatus / nucleus / cytosol / cytoplasm
Similarity search - Function
PARP-10, RNA recognition motif 1 and 2 / PARP14, third RRM domain / : / 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. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-78P / Protein mono-ADP-ribosyltransferase PARP10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Schuler, H.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors.
Authors: Thorsell, A.G. / Ekblad, T. / Karlberg, T. / Low, M. / Pinto, A.F. / Tresaugues, L. / Moche, M. / Cohen, M.S. / Schuler, H.
History
DepositionSep 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 10
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7464
Polymers43,2572
Non-polymers4892
Water6,485360
1
A: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8732
Polymers21,6291
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8732
Polymers21,6291
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 88.677, 58.405
Angle α, β, γ (deg.)90.00, 104.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly [ADP-ribose] polymerase 10 / PARP-10 / ADP-ribosyltransferase diphtheria toxin-like 10 / ARTD10


Mass: 21628.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP10 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q53GL7, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-78P / (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium / Veliparib


Mass: 244.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N4O / Comment: anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 12% PEG3350, 0.1 M Ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2016
RadiationMonochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.25→47.65 Å / Num. obs: 141779 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 20
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKV

3hkv


Resolution: 1.25→47.65 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9377 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.042
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 7066 5 %RANDOM
Rwork0.2079 ---
obs0.2081 141306 99.2 %-
Displacement parametersBiso mean: 20.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.202 Å20 Å20.0143 Å2
2--1.9802 Å20 Å2
3----2.1822 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: 1 / Resolution: 1.25→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 36 360 3456
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113178HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874329HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1454SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes491HARMONIC5
X-RAY DIFFRACTIONt_it3178HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion392SEMIHARMONIC5
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_contact3216SEMIHARMONIC4
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3507 520 5 %
Rwork0.3226 9876 -
all0.3239 10396 -
obs--98.83 %
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)
11.08820.16010.27680.43870.63180.62950.02360.0227-0.1273-0.0535-0.00670.01910.07640.0073-0.01690.00170.00110.0139-0.0253-0.0046-0.018535.4097.132464.9945
20.94411.0699-0.33623.2317-0.44181.1517-0.06790.0216-0.018-0.1929-0.0148-0.2711-0.00250.17560.08270.0238-0.01020.01850.00960.0118-0.002747.182127.7661.0286
30.33920.15070.06330.9306-0.12990.6136-0.0285-0.035-0.01130.0819-0.0149-0.085-0.04540.0510.0434-0.02710.0022-0.0032-0.030.0031-0.037445.568120.709875.4202
40.67120.61620.14791.02350.10180.6957-0.03090.0010.0638-0.11820.05290.0115-0.20140.0751-0.02190.0151-0.02510.0115-0.03150.0006-0.035849.560359.6367.7592
52.7368-0.5339-0.22831.83570.852.4708-0.0236-0.03420.0112-0.20850.01320.19940.0987-0.27060.01040.0085-0.0301-0.0260.00760.02120.000933.080641.364562.0431
60.21120.1582-0.23120.87550.14041.0964-0.0107-0.01740.0380.00150.01560.05140.0014-0.033-0.0048-0.0364-0.00150.0035-0.0305-0.0048-0.031140.07647.795676.7642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|817 - 854}
2X-RAY DIFFRACTION2{A|855 - 879}
3X-RAY DIFFRACTION3{A|880 - 1007}
4X-RAY DIFFRACTION4{B|819 - 862}
5X-RAY DIFFRACTION5{B|863 - 878}
6X-RAY DIFFRACTION6{B|879 - 1007}

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