[English] 日本語
Yorodumi
- PDB-8ptt: Human NUDT5 in complex with MRK-952 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ptt
TitleHuman NUDT5 in complex with MRK-952
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / 8-oxo-GDP phosphatase activity / ADP-ribose diphosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / 8-oxo-GDP phosphatase activity / ADP-ribose diphosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
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
: / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDiaz-Saez, L. / Koekemoer, L. / Feyerherm, C. / Sloman, S. / Fischer, C. / Schneider, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K.V.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: Human NUDT5 in complex with MRK-952
Authors: Diaz-Saez, L. / Koekemoer, L. / Feyerherm, C. / Sloman, S. / Fischer, C. / Schneider, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K.V.M.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,34015
Polymers97,4224
Non-polymers1,91811
Water5,224290
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 49.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)49,6828
Polymers48,7112
Non-polymers9716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-82 kcal/mol
Surface area16580 Å2
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


  • defined by author
  • 49.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)49,6587
Polymers48,7112
Non-polymers9475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-72 kcal/mol
Surface area16530 Å2
Unit cell
Length a, b, c (Å)49.245, 59.679, 81.171
Angle α, β, γ (deg.)78.789, 81.715, 76.034
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
ADP-sugar pyrophosphatase / 8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked ...8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked moiety X motif 5 / hNUDT5 / YSA1H


Mass: 24355.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 (DE3)
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase
#2: Chemical
ChemComp-F2V / 6-[(5~{R})-7-[3-chloranyl-4-(trifluoromethyl)phenyl]-2,7-diazaspiro[4.4]nonan-2-yl]-7-methyl-purine


Mass: 436.861 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H20ClF3N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir: 33% PEG 400, 0.2 M magnesium chloride, and 0.1 M tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.5→28.41 Å / Num. obs: 29822 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.048 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3405 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
REFMAC5.8.0415refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.15 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.815 / ESU R Free: 0.302
RfactorNum. reflection% reflection
Rfree0.2453 1433 4.805 %
Rwork0.178 28389 -
all0.181 --
obs-29822 98.439 %
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: 39.036 Å2
Baniso -1Baniso -2Baniso -3
1-2.431 Å20.788 Å20.886 Å2
2---0.257 Å20.678 Å2
3----1.241 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6062 0 127 290 6479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166084
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.678786
X-RAY DIFFRACTIONr_angle_other_deg0.2891.57314112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8045.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43101102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.94110280
X-RAY DIFFRACTIONr_chiral_restr0.2320.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021313
X-RAY DIFFRACTIONr_nbd_refined0.1860.21047
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.25372
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22931
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2307
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.218
X-RAY DIFFRACTIONr_nbd_other0.1650.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.27
X-RAY DIFFRACTIONr_mcbond_it1.6634.0373169
X-RAY DIFFRACTIONr_mcbond_other1.6624.0373169
X-RAY DIFFRACTIONr_mcangle_it2.8567.2483965
X-RAY DIFFRACTIONr_mcangle_other2.8557.2483966
X-RAY DIFFRACTIONr_scbond_it1.6254.243264
X-RAY DIFFRACTIONr_scbond_other1.6254.243265
X-RAY DIFFRACTIONr_scangle_it2.8257.6964810
X-RAY DIFFRACTIONr_scangle_other2.8257.6964811
X-RAY DIFFRACTIONr_lrange_it4.98939.276746
X-RAY DIFFRACTIONr_lrange_other4.96939.2976711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5640.3081110.2442087X-RAY DIFFRACTION98.4767
2.564-2.6340.3451090.2432008X-RAY DIFFRACTION97.7378
2.634-2.710.291060.2531971X-RAY DIFFRACTION97.7872
2.71-2.7920.348980.2271912X-RAY DIFFRACTION98.6261
2.792-2.8830.267820.2181882X-RAY DIFFRACTION98.2491
2.883-2.9830.264960.2081759X-RAY DIFFRACTION97.8892
2.983-3.0950.2961010.2111774X-RAY DIFFRACTION99.1015
3.095-3.2190.268810.2121650X-RAY DIFFRACTION98.6887
3.219-3.360.256830.2031597X-RAY DIFFRACTION98.1882
3.36-3.5220.248830.1831578X-RAY DIFFRACTION98.4588
3.522-3.7090.226640.171438X-RAY DIFFRACTION99.2074
3.709-3.930.247830.171394X-RAY DIFFRACTION98.7299
3.93-4.1960.187580.1371310X-RAY DIFFRACTION99.1304
4.196-4.5240.264510.1421253X-RAY DIFFRACTION99.0881
4.524-4.9430.181600.1341110X-RAY DIFFRACTION99.0686
4.943-5.5060.23400.1441023X-RAY DIFFRACTION98.4259
5.506-6.3180.223340.175908X-RAY DIFFRACTION98.5356
6.318-7.6440.241430.147749X-RAY DIFFRACTION98.0198
7.644-10.440.156290.126609X-RAY DIFFRACTION99.0683
10.44-28.410.183210.183377X-RAY DIFFRACTION99.005

+
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