[English] 日本語
Yorodumi
- PDB-5lx6: Human PARP10 (ARTD10), catalytic fragment in complex with PARP in... -

+
Open data


ID or keywords:

Loading...

-
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 / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity ...negative regulation of protein K63-linked ubiquitination / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity / NAD+-protein ADP-ribosyltransferase activity / NAD+ 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Veliparib


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


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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}

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more