[English] 日本語
Yorodumi
- PDB-7n13: Crystal structure of MTH1 in complex with compound 32 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n13
TitleCrystal structure of MTH1 in complex with compound 32
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE/HYDROLASE inhibitor / Inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-ZRV / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsEron, S.J.
CitationJournal: Curr Res Chem Biol / Year: 2021
Title: Development of an AchillesTAG degradation system and its application to control CAR-T activity
Authors: Veits, G.K. / Henderson, C.S. / Vogelaar, A. / Eron, S.J. / Lee, L. / Hart, A. / Deibler, R.W. / Baddour, J. / Elam, W.A. / Agafonov, R.V. / Freda, J. / Chaturvedi, P. / Ladd, B. / Carlson, ...Authors: Veits, G.K. / Henderson, C.S. / Vogelaar, A. / Eron, S.J. / Lee, L. / Hart, A. / Deibler, R.W. / Baddour, J. / Elam, W.A. / Agafonov, R.V. / Freda, J. / Chaturvedi, P. / Ladd, B. / Carlson, M.W. / Vora, H.U. / Scott, T.G. / Tieu, T. / Jain, A. / Chen, C.L. / Kibbler, E.S. / Pop, M.S. / He, M. / Kern, G. / Maple, H.J. / Marsh, G.P. / Norley, M.C. / Oakes, C.S. / Henderson, J.A. / Sowa, M.E. / Phillips, A.J. / Proia, D.A. / Park, E.S. / Patel, J.S. / Fisher, S.L. / Nasveschuk, C.G. / Zeid, R.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.country / _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: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,83710
Polymers36,2312
Non-polymers1,6068
Water5,441302
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8224
Polymers18,1161
Non-polymers7073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0146
Polymers18,1161
Non-polymers8995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.607, 67.835, 79.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 3 - 155 / Label seq-ID: 5 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein 7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18115.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-ZRV / 4-anilino-6-[4-(butylcarbamoyl)-3-fluorophenyl]-N-cyclopropyl-7-fluoroquinoline-3-carboxamide


Mass: 514.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28F2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.21 Å3/Da / Density % sol: 44 % / Description: Long needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 23% (w/v) PEG 6k, 200 mM lithium sulfate, 100 mM sodium acetate pH 3.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.59→51.48 Å / Num. obs: 43865 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.59→1.63 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3200 / CC1/2: 0.587 / Rpim(I) all: 0.918 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ANV

5anv


Resolution: 1.59→51.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.798 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.254 2194 5.041 %
Rwork0.2116 41329 -
all0.214 --
obs-43523 99.284 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.759 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0 Å2
2---0.354 Å20 Å2
3---1.433 Å2
Refinement stepCycle: LAST / Resolution: 1.59→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 106 302 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172543
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6373764
X-RAY DIFFRACTIONr_angle_other_deg1.3271.6155873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3395332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63922.583151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.91517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.1930.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22311
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21236
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.214
X-RAY DIFFRACTIONr_nbd_other0.1490.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.219
X-RAY DIFFRACTIONr_mcbond_it1.6791.6171272
X-RAY DIFFRACTIONr_mcbond_other1.6781.6191273
X-RAY DIFFRACTIONr_mcangle_it2.6292.4261600
X-RAY DIFFRACTIONr_mcangle_other2.6292.4221599
X-RAY DIFFRACTIONr_scbond_it2.6161.9381493
X-RAY DIFFRACTIONr_scbond_other2.5661.8911470
X-RAY DIFFRACTIONr_scangle_it4.0862.7922149
X-RAY DIFFRACTIONr_scangle_other4.0252.7152114
X-RAY DIFFRACTIONr_lrange_it5.98419.0963110
X-RAY DIFFRACTIONr_lrange_other5.87618.5733038
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.054726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.131230.05008
12BX-RAY DIFFRACTIONLocal ncs0.131230.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.59-1.6310.4471690.35229850.35732000.5890.65598.56250.336
1.631-1.6760.3221650.32929000.32931040.7770.7798.74360.31
1.676-1.7240.331390.32528580.32530330.7870.77598.81310.303
1.724-1.7770.3481450.30127570.30429410.7880.82298.67390.272
1.777-1.8350.31500.27326990.27428710.8620.87699.23370.238
1.835-1.90.2731360.2725930.2727610.8730.8698.8410.235
1.9-1.9710.3221310.24925250.25226770.850.89699.21550.223
1.971-2.0520.2861240.22224540.22525900.8950.92299.53670.19
2.052-2.1430.244970.20423710.20624750.9230.93599.71720.175
2.143-2.2470.2581290.2122130.21323620.9070.92899.15330.187
2.247-2.3680.2411110.21421210.21522580.930.92698.84850.183
2.368-2.5120.2641030.19620430.19921500.9250.9499.8140.167
2.512-2.6850.2431010.18819120.1920150.9250.94499.90070.165
2.685-2.8990.2221050.18417770.18618830.930.94399.94690.165
2.899-3.1750.2751070.18216450.18717520.9120.951000.167
3.175-3.5480.177800.17615130.17615950.9620.96299.87460.167
3.548-4.0940.206780.15813320.1614120.9570.9799.85840.153
4.094-5.0060.173580.14611550.14712140.9740.97999.91760.143
5.006-7.0460.281410.29240.2039650.9560.971000.19
7.046-51.4820.195250.2135520.2125790.9670.9699.65460.203

+
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