[English] 日本語
Yorodumi
- PDB-6tw7: Leishmania major N-myristoyltransferase in complex with indazole ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tw7
TitleLeishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-918
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / myristoylation / indazole / Leishmania
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
TETRADECANOYL-COA / Chem-NZB / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsBrannigan, J.A.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
CitationJournal: To Be Published
Title: Leishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-918
Authors: Brannigan, J.A.
History
DepositionJan 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5884
Polymers48,1961
Non-polymers1,3933
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-27 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.379, 91.899, 53.609
Angle α, β, γ (deg.)90.000, 113.697, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 48195.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: NMT, LMJF_32_0080 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NZB / [(5-{4-fluoro-2-[2-(pyridin-3-yl)ethoxy]phenyl}-1H-indazol-3-yl)methyl]dimethylamine / 1-[5-[4-fluoranyl-2-(2-pyridin-3-ylethoxy)phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 390.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23FN4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG 1500, 0.2 M NaCl, 0.1 M Na cacodylate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→49 Å / Num. obs: 83675 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 14.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3809 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2434 4182 5.002 %
Rwork0.205 --
all0.207 --
obs-83602 99.205 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.823 Å2-0 Å2-0.286 Å2
2--1.115 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 93 406 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123709
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.6795086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3422.129202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24415621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022911
X-RAY DIFFRACTIONr_nbd_refined0.2140.21738
X-RAY DIFFRACTIONr_nbtor_refined0.320.22500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.239
X-RAY DIFFRACTIONr_mcbond_it2.2672.2561696
X-RAY DIFFRACTIONr_mcangle_it3.043.3822130
X-RAY DIFFRACTIONr_scbond_it2.8792.4932013
X-RAY DIFFRACTIONr_scangle_it4.1123.6282930
X-RAY DIFFRACTIONr_lrange_it5.42331.3825854
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
1.4-1.4360.3592980.36654670.36662140.6980.68392.77440.359
1.436-1.4760.3593270.33357080.33560560.7070.72799.65320.314
1.476-1.5180.3172980.30455790.30558890.7940.80699.79620.279
1.518-1.5650.3062770.2854200.28157120.8420.83799.73740.252
1.565-1.6160.3172840.26852430.27155350.8310.84899.85550.241
1.616-1.6730.312700.25851000.26153780.8430.86799.85120.231
1.673-1.7360.3172620.24949080.25251760.8430.87599.88410.225
1.736-1.8070.2932260.24647420.24949750.8760.88899.85930.227
1.807-1.8870.2732600.22344990.22547660.8950.91499.85310.208
1.887-1.9790.2732180.22943570.23145800.90.91299.89080.217
1.979-2.0860.2542000.22541610.22643740.9140.92299.70280.219
2.086-2.2120.2892120.22538860.22841010.8880.91599.92680.223
2.212-2.3650.2831720.21236850.21538690.8930.91499.68980.214
2.365-2.5540.2361850.19634300.19836320.9310.93999.53190.202
2.554-2.7970.2351630.20131330.20333080.9270.93499.63720.212
2.797-3.1250.211420.19728620.19730170.9320.93899.56910.214
3.125-3.6060.1991250.16925100.17126480.9530.9699.50910.188
3.606-4.4110.21080.14821410.1522610.9540.96799.46930.174
4.411-6.2130.158860.15316620.15317580.9690.97199.43120.186
6.213-49.0890.216690.1869260.1889980.9580.9699.69940.226

+
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