[English] 日本語
Yorodumi
- PDB-3t64: 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t64
Title5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase
Components
  • 5'-(BENZHYDRYLAMINO)-2',5'-DIDEOXYURIDINE
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / dUTP binding / Nucleus / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


tRNA metabolic process / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / DNA replication / magnesium ion binding / identical protein binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. ...Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H.
CitationJournal: Chemmedchem / Year: 2011
Title: Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / ...Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
F: 5'-(BENZHYDRYLAMINO)-2',5'-DIDEOXYURIDINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,76011
Polymers62,1954
Non-polymers1,5657
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-113 kcal/mol
Surface area19810 Å2
MethodPISA
2
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,46110
Polymers61,8973
Non-polymers1,5657
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-111 kcal/mol
Surface area19950 Å2
MethodPISA
3
F: 5'-(BENZHYDRYLAMINO)-2',5'-DIDEOXYURIDINE


  • defined by software
  • 298 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2981
Polymers2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.010, 77.010, 106.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative


Mass: 20632.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: PF11_0282 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8II92, dUTP diphosphatase
#2: Protein/peptide 5'-(BENZHYDRYLAMINO)-2',5'-DIDEOXYURIDINE


Mass: 298.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Chemical ChemComp-DU3 / 2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine


Mass: 393.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H23N3O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.65→36.2 Å / Num. all: 74358 / Num. obs: 74358 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→36.2 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0082refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYQ

1vyq


Resolution: 1.65→34.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.699 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21555 3739 5 %RANDOM
Rwork0.19014 ---
all0.1914 74358 --
obs0.1914 70573 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 107 322 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3352.015036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47324.474152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87215638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9591515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212730
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.52248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53423630
X-RAY DIFFRACTIONr_scbond_it2.22531458
X-RAY DIFFRACTIONr_scangle_it3.6184.51385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 261 -
Rwork0.376 5223 -
obs--100 %

+
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://pdbjlvh1.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