5W4X

Truncated hUGDH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 2.3 of the entry. See complete history

Literature

The entropic force generated by intrinsically disordered segments tunes protein function.

Keul, N.D.Oruganty, K.Schaper Bergman, E.T.Beattie, N.R.McDonald, W.E.Kadirvelraj, R.Gross, M.L.Phillips, R.S.Harvey, S.C.Wood, Z.A.

(2018) Nature 563: 584-588

  • DOI: 10.1038/s41586-018-0699-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein structures are dynamic and can explore a large conformational landscape <sup>1,2 </sup>. Only some of these structural substates are important for protein function (such as ligand binding, catalysis and regulation) <sup>3-5 </sup>. How evolut ...

    Protein structures are dynamic and can explore a large conformational landscape 1,2 . Only some of these structural substates are important for protein function (such as ligand binding, catalysis and regulation) 3-5 . How evolution shapes the structural ensemble to optimize a specific function is poorly understood 3,4 . One of the constraints on the evolution of proteins is the stability of the folded 'native' state. Despite this, 44% of the human proteome contains intrinsically disordered peptide segments greater than 30 residues in length 6 , the majority of which have no known function 7-9 . Here we show that the entropic force produced by an intrinsically disordered carboxy terminus (ID-tail) shifts the conformational ensemble of human UDP-α-D-glucose-6-dehydrogenase (UGDH) towards a substate with a high affinity for an allosteric inhibitor. The function of the ID-tail does not depend on its sequence or chemical composition. Instead, the affinity enhancement can be accurately predicted based on the length of the intrinsically disordered segment, and is consistent with the entropic force generated by an unstructured peptide attached to the protein surface 10-13 . Our data show that the unfolded state of the ID-tail rectifies the dynamics and structure of UGDH to favour inhibitor binding. Because this entropic rectifier does not have any sequence or structural constraints, it is an easily acquired adaptation. This model implies that evolution selects for disordered segments to tune the energy landscape of proteins, which may explain the persistence of intrinsic disorder in the proteome.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. stefano.ciurli@unibo.it.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.,Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602; zaw@uga.edu moremen@uga.edu.,Abteilung molelukare Biowissensschaften, Molekulare Zellbiologie der Pflanzen, Goethe Universität, Frankfurt am Main, Germany.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, 980-8577 Sendai, Japan.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wfeng@ibp.ac.cn.,Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guizhou Medical University, Guiyang, China.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. yingxuxu@shsmu.edu.cn.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA. mmaroney@chem.umass.edu.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA.,the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: ckerfeld@lbl.gov.,JSC Spronk, Vilnius, Lithuania.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Mechanobiology Institute, National University of Singapore, Singapore.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA. zaw@uga.edu.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. jysuh@snu.ac.kr.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada. burrowl@mcmaster.ca.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, Tongji University, Shanghai, China.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.,Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand.,Department of Medicinal Chemistry, Department of Internal Medicine, Comprehensive Cancer Center, and Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A. seongminlee@austin.utexas.edu.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.,Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.,Department of Chemistry, University of Georgia, Athens, GA, USA.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan; miki@kuchem.kyoto-u.ac.jp.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy. stefano.ciurli@unibo.it.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8510 Kyoto, Japan.,Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Sorbonne Université, Collège doctoral, 75005, Paris, France.,Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui 230027, China.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia. Electronic address: r.mcgeary@uq.edu.au.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Institute of Biocomputation and Physics of Complex Systems (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Spain, Department of Biochemistry and Molecular and Cellular Biology, Universidad de Zaragoza, Fundacion ARAID, Gobierno de Aragon, Spain, Aragon Health Research Institute (IIS Aragon), Universidad de Zaragoza, Zaragoza, Spain.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K. jworrall@essex.ac.uk.,State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Howard Hughes Medical Institute, Departments of Physiology and Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.,Drug Discovery Group Cancer Research UK Manchester Institute, Manchester, UK.,the Departments of Life Sciences and.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K. c.dong@uea.ac.uk.,Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,D. E. Shaw Research, New York, NY, USA.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.,Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France.,Structural Biology Research Center, VIB, Brussels, Belgium.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.,the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. howell@sickkids.ca.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan.,Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada. howell@sickkids.ca.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan. jysuh@snu.ac.kr.,Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.,Chemistry and Biochemistry, University of Arizona, 1041 East Lowell Drive, Biosciences West, Tucson, AZ 85281, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, 102-0076 Tokyo, Japan.,Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: ubolsree@biotec.or.th.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. chengq@shsmu.edu.cn.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.,Department of Biochemistry, Western University, London, ON, Canada.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.,National Center for Protein Science Shanghai, Shanghai 201203, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.,Dropbox, New York, NY, USA.,Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France.,Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore.,Bioss Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia.,Medicinal Bioinformatics Center, Shanghai JiaoTong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Department of Biological Chemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, MD9, Singapore.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: penchit@biotec.or.th.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, wipa@sut.ac.th.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France. jacqueline.cherfils@ens-paris-saclay.fr.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Biomedical Sciences, Defence Science and Technology Laboratory Porton Down, SP4 0JQ Salisbury, United Kingdom.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,Max Planck Institute for Plant Breeding Research, Cologne, Germany.,the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-glucose 6-dehydrogenase
A, B, C
466Homo sapiensMutation(s): 0 
Gene Names: UGDH
EC: 1.1.1.22
Find proteins for O60701 (Homo sapiens)
Go to Gene View: UGDH
Go to UniProtKB:  O60701
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG5
Query on PG5

Download SDF File 
Download CCD File 
A, B, C
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 178.190α = 90.00
b = 114.066β = 116.85
c = 97.239γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 2.0: 2017-10-18
    Type: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2018-11-14
    Type: Data collection, Database references
  • Version 2.2: 2018-11-28
    Type: Data collection, Database references
  • Version 2.3: 2018-12-05
    Type: Data collection, Database references