[English] 日本語
Yorodumi
- PDB-5o4v: P.vivax NMT with aminomethylindazole and quinoline inhibitors bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o4v
TitleP.vivax NMT with aminomethylindazole and quinoline inhibitors bound
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / INHIBITOR / MYRISTOYL
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9K2 / ethyl 2,4-dimethylquinoline-3-carboxylate / 2-oxopentadecyl-CoA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsBrannigan, J.A. / Wilkinson, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust087792 United Kingdom
CitationJournal: Nat Chem / Year: 2018
Title: Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus.
Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. ...Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. / Hopkins-Navratilova, I. / Wilkinson, A.J. / Johnston, S.L. / Leatherbarrow, R.J. / Tuthill, T.J. / Solari, R. / Tate, E.W.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,49025
Polymers135,1793
Non-polymers5,31222
Water21,0781170
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8949
Polymers45,0601
Non-polymers1,8358
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7988
Polymers45,0601
Non-polymers1,7387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7988
Polymers45,0601
Non-polymers1,7387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.559, 121.881, 179.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 45059.559 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_085815 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS
References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase

-
Non-polymers , 8 types, 1192 molecules

#2: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


Mass: 991.916 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H64N7O17P3S
#3: Chemical ChemComp-9K2 / 1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 283.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H18FN3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-9KZ / ethyl 2,4-dimethylquinoline-3-carboxylate


Mass: 229.274 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C14H15NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1170 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M AS, 25% PEG 3350, 0.1 M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 139052 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.111 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6801 / CC1/2: 0.36 / Rpim(I) all: 0.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5O48

5o48


Resolution: 1.7→89.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.768 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25757 6874 5 %RANDOM
Rwork0.20712 ---
obs0.20965 130372 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.924 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.7→89.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9406 0 344 1170 10920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0210529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.98814389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43251287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48624.535505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.743151886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3311547
X-RAY DIFFRACTIONr_chiral_restr0.1370.21552
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217983
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_it1.6261.8464736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4142.765961
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3282.0385793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.73725.69917070
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 501 -
Rwork0.381 9685 -
obs--99.97 %

+
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