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- PDB-4f1l: Human Artd8 (Parp14, Bal2) - catalytic domain in complex with inh... -

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Basic information

Entry
Database: PDB / ID: 4f1l
TitleHuman Artd8 (Parp14, Bal2) - catalytic domain in complex with inhibitor A16(Z)
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTransferase/Transferase inhibitor / NAD / ADP-RIBOSE / PARP14 / BAL2 / ARTD8 / ARTD Transferase domain / ADP-ribosylation / Transferase-Transferase inhibitor complex
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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity ...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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / 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-0RY / NITRATE ION / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarlberg, T. / Andersson, C.D. / Lindgren, A. / Spjut, S. / Thorsell, A.G. / Ekblad, T. / Weigelt, J. / Elofsson, M. / Linusson, A. / Schuler, H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening.
Authors: Andersson, C.D. / Karlberg, T. / Ekblad, T. / Lindgren, A.E. / Thorsell, A.G. / Spjut, S. / Uciechowska, U. / Niemiec, M.S. / Wittung-Stafshede, P. / Weigelt, J. / Elofsson, M. / Schuler, H. / Linusson, A.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 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_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: Poly [ADP-ribose] polymerase 14
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,53510
Polymers88,4744
Non-polymers1,0616
Water4,414245
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4153
Polymers22,1191
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3532
Polymers22,1191
Non-polymers2341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4153
Polymers22,1191
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3532
Polymers22,1191
Non-polymers2341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Poly [ADP-ribose] polymerase 14
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7685
Polymers44,2372
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-3 kcal/mol
Surface area17390 Å2
MethodPISA
6
B: Poly [ADP-ribose] polymerase 14
C: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7685
Polymers44,2372
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-3 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.649, 81.894, 83.187
Angle α, β, γ (deg.)60.12, 78.32, 80.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 1534 - 1720 / Label seq-ID: 7 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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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.: 4 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-0RY / (2Z)-4-[(3-carbamoylphenyl)amino]-4-oxobut-2-enoic acid


Mass: 234.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H10N2O4
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% (w/v) polyethylene glycol (PEG) 3350, 0.2 M sodium nitrate, 0.1 M Bis-Tris, 1.3mM A16, pH 5.9, 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: May 19, 2011 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 67716 / Num. obs: 67716 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4926 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SMI

3smi


Resolution: 1.9→34.89 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.192 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 3386 5 %RANDOM
Rwork0.19666 ---
obs0.1988 64330 100 %-
all-64330 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0.09 Å20.08 Å2
2--0.78 Å20.51 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 76 245 6307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226249
X-RAY DIFFRACTIONr_bond_other_d0.0010.024153
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9338496
X-RAY DIFFRACTIONr_angle_other_deg0.9733.00310026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52124.132334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83815948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0091533
X-RAY DIFFRACTIONr_chiral_restr0.1030.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021334
X-RAY DIFFRACTIONr_mcbond_it1.0281.53711
X-RAY DIFFRACTIONr_mcbond_other0.3591.51473
X-RAY DIFFRACTIONr_mcangle_it1.7826010
X-RAY DIFFRACTIONr_scbond_it2.53132538
X-RAY DIFFRACTIONr_scangle_it4.0334.52484
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1049medium positional0.40.5
B1049medium positional0.890.5
C1049medium positional0.490.5
D1049medium positional0.420.5
A1367loose positional0.825
B1367loose positional1.465
C1367loose positional0.875
D1367loose positional0.875
A1049medium thermal1.012
B1049medium thermal1.382
C1049medium thermal1.112
D1049medium thermal1.72
A1367loose thermal1.0410
B1367loose thermal1.2810
C1367loose thermal1.0810
D1367loose thermal1.4910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 245 -
Rwork0.245 4668 -
obs--100 %
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)
10.2699-0.01950.27210.2963-0.06560.93740.00950.00780.0288-0.0017-0.02440.03530.07530.06020.0150.06340.0146-0.00170.01880.01060.02431.0210.3280.459
20.197-0.10120.08030.43240.41220.94130.0477-0.0329-0.0001-0.0346-0.0551-0.01550.0137-0.09130.00740.03840.002900.0436-0.00030.01956.35230.0090.485
30.1365-0.1151-0.15190.5104-0.05891.10320.0015-0.0352-0.0433-0.0408-0.05770.0465-0.07860.05110.05630.0361-0.0106-0.01010.05050.01650.01730.97429.761-33.064
40.18360.11710.16120.22860.15780.93610.026-0.05180.0307-0.0021-0.0352-0.01770.058-0.01840.00920.0096-0.01510.00650.0899-0.00570.0328-3.041-0.122-33.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1534 - 1720
2X-RAY DIFFRACTION2B1532 - 1720
3X-RAY DIFFRACTION3C1534 - 1720
4X-RAY DIFFRACTION4D1534 - 1720

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