[English] 日本語
Yorodumi
- PDB-9qc4: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qc4
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767
ComponentsLysine--tRNA ligase 1
KeywordsLIGASE / inhibitor
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / LYSINE / Lysine--tRNA ligase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsDawson, A. / Cleghorn, L.A.T. / Davis, S.H.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1066891 United States
Bill & Melinda Gates FoundationOPP1191579 United States
Wellcome Trust100195/Z/12/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis.
Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. ...Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. / Ray, P.C. / Epemolu, O. / Lopez-Roman, E.M. / Lopez, L.G. / Engelhart, C.A. / Kim, J. / Pino, P.A. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / Green, S.R. / Cleghorn, L.A.T.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7113
Polymers58,1901
Non-polymers5222
Water55831
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4236
Polymers116,3792
Non-polymers1,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_555-y,-x,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)83.983, 83.983, 147.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Lysine--tRNA ligase 1 / Lysyl-tRNA synthetase 1 / LysRS 1


Mass: 58189.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lysS1, lysS, Rv3598c, MTCY07H7B.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU9, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-A1I5Z / 6-azanyl-1-[2-(azetidin-3-yl)ethyl]-2-cycloheptyl-4-ethoxy-pyrazolo[3,4-d]pyrimidin-3-one


Mass: 374.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.02 % / Description: block
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir: 0.25 M NaOAc, 14% W/V PEG 3350 Protein buffer: 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 25, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→46.275 Å / Num. obs: 16862 / % possible obs: 99.7 % / Redundancy: 13.8 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.062 / Χ2: 0.72 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1964 / CC1/2: 0.972 / Rpim(I) all: 0.222 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→46.275 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.286 / SU ML: 0.317 / Cross valid method: FREE R-VALUE / ESU R: 0.957 / ESU R Free: 0.368
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2921 841 5.004 %
Rwork0.2318 15966 -
all0.235 --
obs-16807 99.638 %
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: 55.198 Å2
Baniso -1Baniso -2Baniso -3
1-2.976 Å20 Å20 Å2
2--2.976 Å20 Å2
3----5.952 Å2
Refinement stepCycle: LAST / Resolution: 2.601→46.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 37 31 3619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123654
X-RAY DIFFRACTIONr_bond_other_d0.0070.0163541
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.8364960
X-RAY DIFFRACTIONr_angle_other_deg0.4131.7618116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.1815.12241
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.506101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5410599
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.66510163
X-RAY DIFFRACTIONr_chiral_restr0.0510.2569
X-RAY DIFFRACTIONr_chiral_restr_other0.0270.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_nbd_refined0.1910.2738
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.23292
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21719
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21963
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0610.225
X-RAY DIFFRACTIONr_nbd_other0.1630.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.218
X-RAY DIFFRACTIONr_mcbond_it2.8825.5631829
X-RAY DIFFRACTIONr_mcbond_other2.875.5621829
X-RAY DIFFRACTIONr_mcangle_it4.6569.9842274
X-RAY DIFFRACTIONr_mcangle_other4.6569.9822275
X-RAY DIFFRACTIONr_scbond_it2.6115.7081825
X-RAY DIFFRACTIONr_scbond_other2.6115.7091824
X-RAY DIFFRACTIONr_scangle_it4.38710.4362684
X-RAY DIFFRACTIONr_scangle_other4.38610.4342685
X-RAY DIFFRACTIONr_lrange_it7.01651.8333933
X-RAY DIFFRACTIONr_lrange_other7.01151.8493931
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
2.601-2.6690.366540.32310920.32512020.9220.92695.34110.297
2.669-2.7410.309600.29311330.29411930.9230.9381000.266
2.741-2.8210.404590.31110980.31711570.9230.931000.284
2.821-2.9070.332710.29810420.30111130.9240.9381000.269
2.907-3.0020.365560.27310470.27811030.9130.9471000.242
3.002-3.1070.35510.25410010.25810520.9240.9561000.227
3.107-3.2240.293590.2419660.24410250.9370.9551000.219
3.224-3.3550.304460.2379310.249770.9320.961000.223
3.355-3.5030.254440.2449190.2449630.9630.9631000.233
3.503-3.6730.246390.2388580.2398970.9690.971000.235
3.673-3.870.282330.2398280.2418610.9360.9651000.237
3.87-4.1030.303320.237920.2338240.9490.9661000.225
4.103-4.3840.307480.1917340.1977820.9330.9771000.199
4.384-4.7320.23420.1836920.1867350.9680.97899.86390.194
4.732-5.1780.316330.2046400.216730.9420.9731000.217
5.178-5.780.248210.2425980.2426190.9580.9691000.251
5.78-6.6570.238330.2355270.2365600.9690.9731000.24
6.657-8.1110.32280.1874530.1934810.9430.9781000.203
8.111-11.2990.171160.1533760.1543920.9720.9841000.187
11.299-46.2750.374160.2772390.2822550.9070.9471000.325

+
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