[English] 日本語
Yorodumi
- PDB-6w65: Human PARP16 in complex with RBN010860 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w65
TitleHuman PARP16 in complex with RBN010860
ComponentsProtein mono-ADP-ribosyltransferase PARP16
KeywordsTRANSFERASE / ADP-RIBOSE / PARP16 / ARTD15 / ARTD Transferase domain / ADP-ribosylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


endoplasmic reticulum tubular network / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / IRE1-mediated unfolded protein response ...endoplasmic reticulum tubular network / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / IRE1-mediated unfolded protein response / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / negative regulation of cytoplasmic translation / endoplasmic reticulum unfolded protein response / nucleotidyltransferase activity / protein serine/threonine kinase activator activity / cellular response to leukemia inhibitory factor / kinase binding / nuclear envelope / viral protein processing / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol
Similarity search - Function
PARP16 N-terminal domain / ARTD15 N-terminal domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Chem-T9D / Protein mono-ADP-ribosyltransferase PARP16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSwinger, K.K. / Wigle, T.J. / Kuntz, K.W.
CitationJournal: Cell Chem Biol / Year: 2020
Title: In Vitro and Cellular Probes to Study PARP Enzyme Target Engagement.
Authors: Wigle, T.J. / Blackwell, D.J. / Schenkel, L.B. / Ren, Y. / Church, W.D. / Desai, H.J. / Swinger, K.K. / Santospago, A.G. / Majer, C.R. / Lu, A.Z. / Niepel, M. / Perl, N.R. / Vasbinder, M.M. ...Authors: Wigle, T.J. / Blackwell, D.J. / Schenkel, L.B. / Ren, Y. / Church, W.D. / Desai, H.J. / Swinger, K.K. / Santospago, A.G. / Majer, C.R. / Lu, A.Z. / Niepel, M. / Perl, N.R. / Vasbinder, M.M. / Keilhack, H. / Kuntz, K.W.
History
DepositionMar 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP16
B: Protein mono-ADP-ribosyltransferase PARP16
C: Protein mono-ADP-ribosyltransferase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,23224
Polymers93,3323
Non-polymers2,90121
Water5,026279
1
A: Protein mono-ADP-ribosyltransferase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1118
Polymers31,1111
Non-polymers1,0017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mono-ADP-ribosyltransferase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,37211
Polymers31,1111
Non-polymers1,26110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein mono-ADP-ribosyltransferase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7495
Polymers31,1111
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.120, 147.120, 99.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-472-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 3 - 274 / Label seq-ID: 1 - 272

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Protein mono-ADP-ribosyltransferase PARP16 / ADP-ribosyltransferase diphtheria toxin-like 15 / Poly [ADP-ribose] polymerase 16 / PARP-16


Mass: 31110.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP16, ARTD15, C15orf30 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N5Y8, Transferases; Glycosyltransferases; Pentosyltransferases

-
Non-polymers , 6 types, 300 molecules

#2: Chemical ChemComp-T9D / 5-{5-[(piperidin-4-yl)oxy]-2H-isoindol-2-yl}-4-(trifluoromethyl)pyridazin-3(2H)-one


Mass: 378.348 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H17F3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium citrate pH5.5, 18%w/v PEG3350

-
Data collection

DiffractionMean temperature: 63 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→37.78 Å / Num. obs: 58280 / % possible obs: 99.87 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.6
Reflection shellResolution: 2.13→2.185 Å / Rmerge(I) obs: 0.948 / Num. unique obs: 4242

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→37.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.942 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.159
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 3047 5 %RANDOM
Rwork0.1901 ---
obs0.1919 58280 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.68 Å2 / Biso mean: 55.531 Å2 / Biso min: 26.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: final / Resolution: 2.13→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 197 279 6113
Biso mean--74.69 52.59 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136056
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175586
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.658201
X-RAY DIFFRACTIONr_angle_other_deg1.3131.58812970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1915725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7921.944288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82415968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.581530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021291
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70140.12
12B70140.12
21A70070.11
22C70070.11
31B68680.12
32C68680.12
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 217 -
Rwork0.291 4242 -
all-4459 -
obs--99.62 %

+
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