6H9X

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily.

De Ruysscher, D.Pang, L.De Graef, S.Nautiyal, M.De Borggraeve, W.M.Rozenski, J.Strelkov, S.V.Weeks, S.D.Van Aerschot, A.

(2019) Eur.J.Med.Chem. 174: 252-264

  • DOI: 10.1016/j.ejmech.2019.04.045

  • PubMed Abstract: 
  • The superfamily of adenylate-forming enzymes all share a common chemistry. They activate a carboxylate group, on a specific substrate, by catalyzing the formation of a high energy mixed phosphoanhydride-linked nucleoside intermediate. Members of this ...

    The superfamily of adenylate-forming enzymes all share a common chemistry. They activate a carboxylate group, on a specific substrate, by catalyzing the formation of a high energy mixed phosphoanhydride-linked nucleoside intermediate. Members of this diverse enzymatic family play key roles in a variety of metabolic pathways and therefore many have been regarded as drug targets. A generic approach to inhibit such enzymes is the use of non-hydrolysable sulfur-based bioisosteres of the adenylate intermediate. Here we compare the activity of compounds containing a sulfamoyl and sulfonamide linker respectively. An improved synthetic strategy was developed to generate inhibitors containing the latter that target isoleucyl- (IleRS) and seryl-tRNA synthetase (SerRS), two structurally distinct representatives of Class I and II aminoacyl-tRNA synthetases (aaRSs). These enzymes attach their respective amino acid to its cognate tRNA and are indispensable for protein translation. Evaluation of the ability of the two similar isosteres to inhibit serRS revealed a remarkable difference, with an almost complete loss of activity for seryl-sulfonamide 15 (SerSoHA) compared to its sulfamoyl analogue (SerSA), while inhibition of IleRS was unaffected. To explain these observations, we have determined a 2.1 Å crystal structure of Klebsiella pneumoniae SerRS in complex with SerSA. Using this structure as a template, modelling of 15 in the active site predicts an unfavourable eclipsed conformation. We extended the same modelling strategy to representative members of the whole adenylate-forming enzyme superfamily, and were able to disclose a new classification system for adenylating enzymes, based on their protein fold. The results suggest that, other than for the structural and functional orthologues of the Class II aaRSs, the O to C substitution within the sulfur-sugar link should generally preserve the inhibitory potency.


    Organizational Affiliation

    Department of Medicine , University of Wisconsin-Madison , 3341 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio. rosa.lapalombella@osumc.edu john.byrd@osumc.edu.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA. Michael.Acker@novartis.com.,The RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sato-gun, Hyogo, 678-5248, Japan.,the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.,School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,iHuman Institute, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. Electronic address: lidefeng@im.ac.cn.,Department of Hematology, Hôpital Necker, Assistance Publique Hôpitaux de Paris, University Paris Descartes, 75006 Paris, France.,Structural Biology and Biochemistry program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India sgourinath@mail.jnu.ac.in.,William S. Middleton Memorial Veterans Hospital , 2500 Overlook Terr. , Madison , Wisconsin 53705 , United States.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Centre de Génomique Fonctionnelle Bordeaux, Université Bordeaux, F-33076, Bordeaux, France.,Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.,Departments of Biochemistry and Biophysics and Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Medical Microbiology and Immunology , University of Wisconsin-Madison , 4203 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Bioorganic Chemistry and Bio-Crystallography laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy. Electronic address: stefano.benini@unibz.it.,Division of Cell Signaling and Immunology and University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.,Xtal BioStructures Inc., Natick, MA 01760, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.,Department of Pharmacology, Monash University, Clayton, VIC 3800, Australia.,CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. sunlf17@ustc.edu.cn.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia. Electronic address: M.Maher@latrobe.edu.au.,Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Clinical Medicine, Aarhus University, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark.,Small Molecule Screening Facility, Carbone Cancer Center , University of Wisconsin-Madison , 1111Highland Ave. , Madison , Wisconsin 53705 , United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. mirko.zaffagnini3@unibo.it.,Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716; zzhuang@udel.edu ytong@uwindsor.ca.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Paris Saclay, 91190 Paris, France.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. michelet@ibpc.fr.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.,Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084 China.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.,Chemical Synthesis Core, Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany.,College of Veterinary Medicine, The Ohio State University, Columbus, Ohio.,HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK g.l.challis@warwick.ac.uk.,KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. lemaire@ibpc.fr.,KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Biocrystallography, Herestraat 49 BOX 822, 3000 Leuven, Belgium.,From the Department of Biochemistry and Molecular Biology, ncjs@mail.ubc.ca.,Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. crozet@ibpc.fr.,Center for Biostatistics, The Ohio State University, Columbus, Ohio.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio.,3Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China.,ESRF, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble CS 40220, France.,5Present Address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,iHuman Institute, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, USA.,the Centre for Blood Research, and.,Department of Pathology, St. Olavs Hospital, Trondheim, Norway.,School of Medicine and Dentistry , University of Rochester Medical Center , 601 Elmwood Ave. , Rochester , New York 14620 , United States.,Biomedical Center, Ludwig-Maximilians-University Munich (LMU), 82152, Martinsried, Germany.,Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.,Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, Trieste 34149, Italy.,KU Leuven, Department of Chemistry, Molecular Design and Synthesis, Celestijnenlaan 200F BOX 2404, 3001 Leuven, Belgium.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; zzhuang@udel.edu ytong@uwindsor.ca.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.,Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia.,Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland.,LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse 6, Marburg 35032, Germany.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Fisheries College, Guangdong Ocean University, Zhanjiang, 524025 Guangdong, China.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia.,LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. Electronic address: jsunkim@chonnam.ac.kr.,Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, 97074, Germany.,Department of Medicine , Vanderbilt-Ingram Cancer Center , Nashville , Tennessee 37232 , United States.,Department of Biochemistry , Vanderbilt University School of Medicine , 2215 Garland Avenue, 607 Light Hall , Nashville , Tennessee 37232-0146 , United States.,Bio-Pharmaceutical Analysis Section (Bio-PhASe), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy. daniele.tedesco@unibo.it.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Cell and Molecular Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States.,Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: dcwang@ibp.ac.cn.,Plexxikon Inc., Berkeley, California.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Sorbonne Paris Cité, Paris, France.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, DK-8000, Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark.,Biocenter, Faculty of Biology, Genetics, Ludwig-Maximilians-University Munich (LMU), 82152, Martinsried, Germany.,Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.,INSERM U944, Institute of Hematology, St. Louis Hospital, 75010 Paris, France.,Department of Picobiology/Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.,Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. julien.henri@sorbonne-universite.fr.,Queensland Brain Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands. b.j.c.janssen@uu.nl.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus C, Denmark. pn@mbg.au.dk.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,MRC, Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, U.K.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Germany.,Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.,Max Planck-Institute for Biochemistry, 82152, Martinsried, Germany.,Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,4Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX), Germany.,From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.,Department of Dermatology, Aarhus University Hospital, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark.,Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan.,Biocenter, Faculty of Biology, Genetics, Ludwig-Maximilians-University Munich (LMU), 82152, Martinsried, Germany. boshart@lmu.de.,Department of Hematology and Oncology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Membrane Biology, Beijing, 100084 China.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, USA.,From the Department of Biochemistry and Molecular Biology.,Leidos Biomedical Research , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21701 , United States.,Department of Chemistry "Giacomo Ciamician", University of Bologna, via Selmi 2, 40126 Bologna, Italy. simona.fermani@unibo.it.,Department of Clinical Medicine, Aarhus University, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark. lars.iversen@clin.au.dk.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,the Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and.,Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; l.rash@uq.edu.au glenn.king@imb.uq.edu.au.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR47UH, United Kingdom.,From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 wilson5@niehs.nih.gov.,BIOLOG Life Science Institute, 28199, Bremen, Germany.,Department of Medicine, University of California San Diego, La Jolla, California, United States of America.,Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA. kapplerj@njhealth.org shaodong.dai@ucdenver.edu.,Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA.,Medical Research Council Protein Phosphorylation Unit, School of Life Sciences, Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada.,School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.,KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium. Electronic address: arthur.vanaerschot@kuleuven.be.,Cayman Chemical Co., Ann Arbor, MI 48108, USA.,KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium; KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Biocrystallography, Herestraat 49 BOX 822, 3000 Leuven, Belgium.,Bioorganic Chemistry and Bio-Crystallography laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Dermatology, Aarhus University Hospital, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark. lars.iversen@clin.au.dk.,Benaroya Research Institute, Seattle, WA 98101, USA.,Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.,Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , SGC Center for Chemical Biology, 120 Mason Farm Rd. , Chapel Hill , North Carolina 27599 , United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,National Cancer Institute , Bethesda , Maryland 20892 , United States.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine--tRNA ligase
A
430Klebsiella pneumoniaeMutation(s): 0 
Gene Names: serS (serS_1, serS_2)
EC: 6.1.1.11
Find proteins for W9BNU9 (Klebsiella pneumoniae)
Go to UniProtKB:  W9BNU9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA
Query on SSA

Download SDF File 
Download CCD File 
A
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.407α = 90.00
b = 84.407β = 90.00
c = 229.874γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG077814N
Research Foundation - FlandersBelgiumG0A4616N
Research Foundation - FlandersBelgium1109117N

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release