Skip to main content
SpringerLink
Log in
Book cover

Essentials of Bioinformatics, Volume I pp 47–73Cite as

Biological 3D Structural Databases

  • Chapter
  • First Online:

Abstract

Structural biology is a branch of biological sciences that deals with the molecular structure of biological macromolecule structures like proteins, DNA, and RNA. Getting acquainted with spatial positions of the molecular atoms, the cavities, channels, pores, and clefts found in the macromolecular structure can explain many phenomena such as the mechanisms of protein-protein interaction, inhibition or activation of cellular receptors, antibiotic resistance, and other cellular mysteries. Designing new drugs is mostly facilitated via 3D information of the target receptor. The 3D structures can be elucidated using four major techniques, X-ray, NMR spectroscopy, cryo-electron microscopy (cryo-EM), and neutron diffraction, given that each of these techniques has its merits and demerits. Maintaining these invaluable and exponentially growing structural data is a crucial step. Therefore, data repositories known as structural databases are created where a plethora of structures are deposited and refined yearly. This chapter presents these databases and highlights their characteristic features in addition to related servers that help in storing, analysis, comparison, and classification of the 3D structural information such as RCSB PDB, PDBj, PDBe, BMRB, SCOP2, CATH, PDBsum, sc-PDB, and PDBTM.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R (2014) PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun 445(4):717–723

    CAS  PubMed  PubMed Central  Google Scholar 

  • An J, Totrov M, Abagyan R (2005) Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 4(6):752–761

    CAS  PubMed  Google Scholar 

  • Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2007) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36(suppl_1):D419–D425

    PubMed  PubMed Central  Google Scholar 

  • Babajan B, Chaitanya M, Rajsekhar C, Gowsia D, Madhusudhana P, Naveen M et al (2011) Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors. Interdiscip Sci 3(3):204–216. https://doi.org/10.1007/s12539-011-0100-y

    Article  CAS  PubMed  Google Scholar 

  • Bagchi A (2012) A brief overview of a few popular and important protein databases. Computat Mol Biosci 2(04):115

    Google Scholar 

  • Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J (2000) The Protein Data Bank and the challenge of structural genomics. Nat Struct Mol Biol 7:957–959

    CAS  Google Scholar 

  • Berman HM, Kleywegt GJ, Nakamura H, Markley JL (2012) The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure 20(3):391–396

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581–586

    CAS  PubMed  PubMed Central  Google Scholar 

  • Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2013) The nucleic acid database: new features and capabilities. Nucleic Acids Res 42(D1):D114–D122

    PubMed  PubMed Central  Google Scholar 

  • Craveur P, Rebehmed J, de Brevern AG (2014) PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. Database:2014

    Google Scholar 

  • Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P et al (2016) CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 45(D1):D289–D295

    PubMed  PubMed Central  Google Scholar 

  • Dawson NL, Sillitoe I, Lees JG, Lam SD, Orengo CA (2017) CATH-Gene3d: generation of the resource and its use in obtaining structural and functional annotations for protein sequences. Protein Bioinforma 1558:79–110

    CAS  Google Scholar 

  • DeLano WL (2002) The PyMOL molecular graphics system. http://pymol.org

  • Desaphy J, Bret G, Rognan D, Kellenberger E (2014) sc-PDB: a 3D-database of ligandable binding sites—10 years on. Nucleic Acids Res 43(D1):D399–D404

    PubMed  PubMed Central  Google Scholar 

  • Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66(4):486–501

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gaber Y (2016) In-silico smart library design to engineer a xylosetolerant hexokinase variant. Afr J Biotechnol 15(21):910–916

    CAS  Google Scholar 

  • Gaber Y, Mekasha S, Vaaje-Kolstad G, Eijsink VG, Fraaije MW (2016) Characterization of a chitinase from the cellulolytic actinomycete Thermobifida fusca. Biochim Biophys Acta 1864(9):1253–1259

    CAS  PubMed  Google Scholar 

  • Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E (2016) The ChEMBL database in 2017. Nucleic Acids Res 45(D1):D945–D954

    PubMed  PubMed Central  Google Scholar 

  • Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C (2015) ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res 44(D1):D1214–D1219

    PubMed  PubMed Central  Google Scholar 

  • Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38(suppl_2):W545–W549

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hubbard TJ, Murzin AG, Brenner SE, Chothia C (1997) SCOP: a structural classification of proteins database. Nucleic Acids Res 25(1):236–239

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jo S, Im W (2012) Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res 41(D1):D470–D474

    PubMed  PubMed Central  Google Scholar 

  • Joosten RP, Te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R et al (2010) A series of PDB related databases for everyday needs. Nucleic Acids Res 39(suppl_1):D411–D419

    PubMed  PubMed Central  Google Scholar 

  • Kellenberger E, Muller P, Schalon C, Bret G, Foata N, Rognan D (2006) sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model 46(2):717–727

    CAS  PubMed  Google Scholar 

  • Kinjo AR, Bekker G-J, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H (2016) Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res 45:D282–D288. https://doi.org/10.1093/nar/gkw962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knudsen M, Wiuf C (2010) The CATH database. Hum Genomics 4(3):207

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kozma D, Simon I, Tusnady GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res 41(D1):D524–D529

    PubMed  PubMed Central  Google Scholar 

  • Krieger E, Vriend G (2014) YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics 30(20):2981–2982

    CAS  PubMed  PubMed Central  Google Scholar 

  • Laskowski RA (2007) Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics 23(14):1824–1827

    CAS  PubMed  Google Scholar 

  • Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM (2018) PDBsum: structural summaries of PDB entries. Protein Sci 27(1):129–134

    CAS  PubMed  Google Scholar 

  • Ledford H (2010) Big science: the cancer genome challenge. Nat News 464(7291):972–974

    CAS  Google Scholar 

  • Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res 28(1):257–259

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, Galzitskaya OV (2009) ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Res 38(suppl_1):D283–D287

    PubMed  PubMed Central  Google Scholar 

  • Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH (2013) MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res 42(D1):D297–D303

    PubMed  PubMed Central  Google Scholar 

  • Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40(3):153–155

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mewes H-W, Frishman D, Güldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Münsterkötter M, Rudd S, Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30(1):31–34

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pavelka A, Chovancova E, Damborsky J (2009) HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res 37(suppl_2):W376–W383

    CAS  PubMed  PubMed Central  Google Scholar 

  • Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North A (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-Å resolution obtained by X-ray analysis. Nature 185(4711):416

    CAS  PubMed  Google Scholar 

  • Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics 11(1):231

    PubMed  PubMed Central  Google Scholar 

  • Putignano V, Rosato A, Banci L, Andreini C (2017) MetalPDB in 2018: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 46(D1):D459–D464

    PubMed Central  Google Scholar 

  • Rosenbaum DM, Rasmussen SG, Kobilka BK (2009) The structure and function of G-protein-coupled receptors. Nature 459(7245):356

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11(9):739–747

    CAS  PubMed  Google Scholar 

  • Shindyalov IN, Bourne PE (2001) A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res 29(1):228–229

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MS (2015) MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes. Structure 23(7):1350–1361

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J et al (2007) BioMagResBank. Nucleic Acids Res 36(suppl_1):D402–D408

    PubMed  PubMed Central  Google Scholar 

  • Varadi M, Tompa P (2015) The protein ensemble database. Intrinsically disordered proteins studied by NMR spectroscopy. Springer, pp 335–349

    Google Scholar 

  • Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S et al (2010) PDBe: protein data bank in Europe. Nucleic Acids Res 39(suppl_1):D402–D410

    PubMed  PubMed Central  Google Scholar 

  • Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P (2015) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44(D1):D385–D395

    PubMed  PubMed Central  Google Scholar 

  • Wang XT, Chan TF, Lam V, Engel PC (2008) What is the role of the second “structural” NADP+-binding site in human glucose 6-phosphate dehydrogenase? Protein Sci 17(8):1403–1411

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275(1):1–21

    CAS  PubMed  Google Scholar 

  • Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA (2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res 34(suppl_1):D281–D284

    CAS  PubMed  Google Scholar 

  • Yin H, Flynn AD (2016) Drugging membrane protein interactions. Annu Rev Biomed Eng 18:51

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zanegina O, Kirsanov D, Baulin E, Karyagina A, Alexeevski A, Spirin S (2015) An updated version of NPIDB includes new classifications of DNA–protein complexes and their families. Nucleic Acids Res 44(D1):D144–D153

    PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University, Al-Karak, Jordan

    Yasser Gaber

  2. Microbiology Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt

    Yasser Gaber

  3. Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt

    Boshra Rashad & Eman Fathy

  4. Microbiology Department, Directorate of Health Affairs at Ministry of Health, Beni-Suef, Egypt

    Eman Fathy

Authors
  1. Yasser Gaber
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Boshra Rashad
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eman Fathy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yasser Gaber .

Editor information

Editors and Affiliations

  1. Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Noor Ahmad Shaik

  2. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Khalid Rehman Hakeem

  3. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Babajan Banaganapalli

  4. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Ramu Elango

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Gaber, Y., Rashad, B., Fathy, E. (2019). Biological 3D Structural Databases. In: Shaik, N., Hakeem, K., Banaganapalli, B., Elango, R. (eds) Essentials of Bioinformatics, Volume I. Springer, Cham. https://doi.org/10.1007/978-3-030-02634-9_4

Download citation

Publish with us

Policies and ethics

Search

Navigation