[English] 日本語
Yorodumi
- PDB-7nr6: Structure of NUDT15 in complex with NSC56456 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nr6
TitleStructure of NUDT15 in complex with NSC56456
ComponentsProbable 8-oxo-dGTP diphosphatase NUDT15
KeywordsHYDROLASE / Inhibitor / complex / Nucleoside Triphosphate Pyrophosphohydrolase
Function / homology
Function and homology information


nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / regulation of proteasomal protein catabolic process / xenobiotic catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol
Similarity search - Function
NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione / Nucleotide triphosphate diphosphatase NUDT15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRehling, D. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: To Be Published
Title: Coupling cellular target engagement to drug-induced responses with CeTEAM
Authors: Valerie, N.C.K. / Rehling, D. / Stenmark, P.
History
DepositionMar 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable 8-oxo-dGTP diphosphatase NUDT15
B: Probable 8-oxo-dGTP diphosphatase NUDT15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9418
Polymers37,2702
Non-polymers6716
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-24 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.843, 49.032, 135.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Probable 8-oxo-dGTP diphosphatase NUDT15 / 8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / ...8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / Nucleoside diphosphate-linked moiety X motif 15 / Nudix motif 15


Mass: 18635.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, nucleotide diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UO8 / 2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione


Mass: 249.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2M sodium acetate, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→67.69 Å / Num. obs: 29634 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.919 / Num. unique obs: 1714 / CC1/2: 0.757 / Rpim(I) all: 0.371 / Rrim(I) all: 0.993

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BON

5bon


Resolution: 1.8→67.69 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 1419 4.81 %
Rwork0.1872 28109 -
obs0.1882 29528 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 44 284 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572629
X-RAY DIFFRACTIONf_angle_d0.82243575
X-RAY DIFFRACTIONf_chiral_restr0.061357
X-RAY DIFFRACTIONf_plane_restr0.0055494
X-RAY DIFFRACTIONf_dihedral_angle_d13.5813975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.29581300.24732767X-RAY DIFFRACTION99.52
1.86-1.940.27981430.23132766X-RAY DIFFRACTION99.11
1.94-2.030.22591480.21432731X-RAY DIFFRACTION99
2.03-2.130.24631190.19942828X-RAY DIFFRACTION99.83
2.13-2.270.22021260.20542793X-RAY DIFFRACTION99.83
2.27-2.440.241370.20922796X-RAY DIFFRACTION99.19
2.44-2.690.21591500.20612780X-RAY DIFFRACTION99.49
2.69-3.080.21311540.20332837X-RAY DIFFRACTION99.67
3.08-3.880.1951450.16132861X-RAY DIFFRACTION99.34
3.88-67.690.17091670.16382950X-RAY DIFFRACTION98.39
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)
13.253242045431.13150392018-0.4258774066711.520779577580.6053697113282.077112235030.002244067644430.2940732887540.0214363805442-0.0926415742331-0.01245157112730.3625114675870.338012804671-0.483033750645-0.02809263717440.1786280529480.023088780170.0154802229280.1269742891420.01923654356950.11198373170552.708694193655.3900957245289.63470132
22.688179475180.966908443792-1.047635802442.24848426538-0.4479682930681.01272991107-0.01594070030490.06762875683580.2834950786440.0684081950560.1267685820680.2090806371430.0451586240981-0.1536112506530.02684406339790.1212027572960.02274259092470.004691918160110.1059717955090.01977769136890.13600982328256.439969552863.2741833426293.438963241
31.372670801621.307751589770.2655718639381.1574817353-0.5308342909032.17162139911-0.04928480562630.143801202868-0.188738842418-0.05427017482830.1144089979550.2080088641460.241026894004-0.565066240636-0.005878019079760.241782214794-0.02327710239310.008744324245970.2806537851710.0188206701080.1801357895749.312397799550.7390366677290.389098599
42.071416298531.34894726084-0.5790536323981.512668997670.2270505961130.889302184078-0.1308265224770.189457704694-0.181442841904-0.2453567848160.126429811948-0.1444907975290.2905305044440.124143977311-5.79703962965E-70.229462112630.02463081344710.01700308887450.1993605226640.01429212530290.18915624352664.789216649157.2274159245283.235627036
52.273149053511.31564802964-0.8274936939281.86834775146-0.6992368998142.854677739730.0121537662960.2384353245830.400884848270.004432036005370.1169543539130.25928764019-0.3274761286760.09815946490250.0370150466760.1414076087210.00776489381092-0.00225336029370.1383982546460.05258379941730.18420964516873.024998913277.7005561238281.145418845
61.17456971531-0.1918362630340.1467145608980.378469588776-0.5673252991880.9295291934230.0690812877561-0.02894069450291.053037080690.3585524481820.1591329282190.037925709673-0.6535421295060.3011242074850.09325622295770.311992798220.01497007910260.07757596437590.0874878565433-0.0462285484530.44932125993265.84538932878.3424097411291.168928083
71.463709687020.462310855047-0.3779248479921.188054158330.02631143693561.841128341950.1079626457570.0684993524160.2354127375270.01135176537030.0395274056336-0.0947458613694-0.4271969312610.4763515395050.01005307030060.268275985845-0.07427233880440.04709553849380.2315677336460.03378077137460.22009506911981.938579532282.8929507632280.78618401
81.637041306251.62475278416-0.2625743203581.60597404908-0.7850554828051.264045549250.0433032531449-0.1949237565670.00967049527440.0872632949508-0.0558884479916-0.110814352423-0.09070461148630.356737757477-5.26582934861E-70.2075748800080.00793925002932-0.01826832360270.2449031982550.008885082976430.21113609949875.466521335270.3764502446292.610255052
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 11:45)AA11 - 451 - 35
22(chain A and resid 46:105)AA46 - 10536 - 98
33(chain A and resid 106:134)AA106 - 13499 - 127
44(chain A and resid 135:163)AA135 - 163128 - 156
55(chain B and resid 11:84)BE11 - 841 - 77
66(chain B and resid 85:99)BE85 - 9978 - 92
77(chain B and resid 100:132)BE100 - 13293 - 125
88(chain B and resid 133:163)BE133 - 163126 - 156

+
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