[English] 日本語
Yorodumi
- PDB-6c9r: Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c9r
TitleMycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol
ComponentsAdenosine kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Nucleoside analog / Complex / Inhibitor / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / dGTP binding / AMP salvage / purine ribonucleoside salvage / phosphorylation / GTP binding / magnesium ion binding / ATP binding / plasma membrane
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ERJ / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCrespo, R.A. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1024055 United States
Welch FoundationA-0015 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01A1095208 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase.
Authors: Crespo, R.A. / Dang, Q. / Zhou, N.E. / Guthrie, L.M. / Snavely, T.C. / Dong, W. / Loesch, K.A. / Suzuki, T. / You, L. / Wang, W. / O'Malley, T. / Parish, T. / Olsen, D.B. / Sacchettini, J.C.
History
DepositionJan 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / 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
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4379
Polymers71,9612
Non-polymers1,4757
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Sedimentation coefficient
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-29 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.236, 81.984, 158.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Adenosine kinase / / AK


Mass: 35980.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK, cbhK, MRA_2218 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4N0, UniProt: P9WID5*PLUS, adenosine kinase
#2: Chemical
ChemComp-ERJ / 9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine


Mass: 334.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H14N4O4S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 5.0 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.102→44.38 Å / Num. obs: 57583 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.05875 / Net I/σ(I): 11.89
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.3148 / Mean I/σ(I) obs: 3.43 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKM

2pkm


Resolution: 2.1→44.38 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.62
RfactorNum. reflection% reflection
Rfree0.204 2942 5.11 %
Rwork0.181 --
obs0.182 57558 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 82 276 5416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085245
X-RAY DIFFRACTIONf_angle_d0.7817135
X-RAY DIFFRACTIONf_dihedral_angle_d14.2773022
X-RAY DIFFRACTIONf_chiral_restr0.051814
X-RAY DIFFRACTIONf_plane_restr0.005924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1024-2.13690.23791290.21682443X-RAY DIFFRACTION96
2.1369-2.17370.2511360.19642560X-RAY DIFFRACTION100
2.1737-2.21330.23361180.19562602X-RAY DIFFRACTION100
2.2133-2.25580.25641330.19712580X-RAY DIFFRACTION100
2.2558-2.30190.2491370.20182555X-RAY DIFFRACTION100
2.3019-2.35190.27651460.1952588X-RAY DIFFRACTION100
2.3519-2.40660.20271340.1912564X-RAY DIFFRACTION100
2.4066-2.46680.22831510.18792572X-RAY DIFFRACTION100
2.4668-2.53350.21771460.18572574X-RAY DIFFRACTION100
2.5335-2.60810.20721430.18742573X-RAY DIFFRACTION100
2.6081-2.69220.23061450.19522584X-RAY DIFFRACTION100
2.6922-2.78840.21771440.19532600X-RAY DIFFRACTION100
2.7884-2.90010.21561540.20162563X-RAY DIFFRACTION100
2.9001-3.0320.23031510.20012605X-RAY DIFFRACTION100
3.032-3.19180.23551390.19442595X-RAY DIFFRACTION100
3.1918-3.39180.20611460.1862620X-RAY DIFFRACTION100
3.3918-3.65350.20481420.16762610X-RAY DIFFRACTION100
3.6535-4.0210.17451110.15272668X-RAY DIFFRACTION100
4.021-4.60240.1611420.14042658X-RAY DIFFRACTION100
4.6024-5.79660.15541390.15952703X-RAY DIFFRACTION100
5.7966-45.41790.21081560.21082799X-RAY DIFFRACTION100

+
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