by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  

  • Search for a PDB/NDB entry via PDB or NDB code
    Code examples:
    - PDB: 3CRO; NDB: PDR001

  • Search the Hetero Components Database.
  • Search for a PDB/NDB entry via SWISS-PROT or SMART or Pfam
    This is a
      SWISS-PROT entry name/accession number
    or a
      SWISS-PROT species name
    or a
      SWISS-PROT gene name
    or a
      SWISS-PROT entry description
    or a
      Pfam family name
    or a
      SMART domain name

    Except for the gene name at least three characters are required.
    Wildcards are automatically added before or after the search string.
    In case of gene names the search string can consist of one or two characters only. In this case a wildcard search is only possible for at least three characters and has to be specifically indicated by the wildcard sign '%'.
    - SWISS-PROT entry name - RCRO_BP434; - SWISS-PROT accession number - P03036.
    Hint:Type RCRO_ to get all PDB entries of the REGULATORY PROTEIN CRO and type _BP434 to get all PDB entries for the BACTERIOPHAGE 434.
    - SWISS-PROT species name - Populus nigra
    - SWISS-PROT gene name - petE
    Hint: Use the wildcard sign '%' (with at least three valid characters), e.g. pet%, to identify all PDB structures containing gene products of the photosynthetic electron transfer genes
    - SWISS-PROT entry description - Cytochrome F or EC
    In addition to the protein name the entry description also includes the enzyme classification.
    By searching for 'EC 1.' you will find all oxidoreductases and a search for 'EC 3.4.19'. returns all omega peptidases (for which 3D structures with an SWISS-PROT entry name/accession number assigned are known). When searching for EC numbers at least one dot has to be given. One can, however, skip the blank after EC. If one skips EC and searches for '1.9', for example, the hits are EC, EC, EC, 1.9.3, ...
    There are 6 basic enzyme classes:
    EC 1. (Oxidoreductases), EC 2. (Transferases), EC 3. ( Hydrolases), EC 4. (Lyases), EC 5. (Isomerases) and EC 6. (Ligases).
    More detailed information on the enzyme classification can be found here.
    - Pfam family name - A search for pkinase returns all PDB structures with a pkinase domain (for example 1fvr with the domains EGF|fn3|pkinase or many structures with the domains SH2|SH3|pkinase and so on).
    - SMART domain name - A search for TyrKc returns all PDB structures with a TyrKc domain (for example 1fvr with the domains EGF|EGF_like|FN3|TyrKc or many structures with the domains SH2|SH3|TyrKc and so on).

  • Browse the PDB/SWISS-PROT cross reference lists.
  • The SCOP database can be queried by
    • sunid (This SCOP unique identifier consists of 5 digits, e.g. 49507 for the protein domain Plastocyanin. It uniquely identifies any entries in the SCOP hierarchy).
    • sccs (This set of concise classification strings is associated with the most relevant hierarchical levels. For example in d.126.1.1., d stands for the class, 126 for the fold and the remaining two 1 for superfamily and family).
    • keywords

    The keyword search can either be performed for protein domain, family, superfamily, fold, class names or for the comments.
    Protein domain, family, superfamily, fold, class search:
    Search for hemoglobin gives only results for Hemoglobin, whereas due to the usage of the wildcard sign % search for %hemoglobin% gives also Truncated hemoglobin or Leghemoglobin, for example.
    Boolean keyword combinations are not possible. You can, however, search for strings that correspond exactly to SCOP descriptions, such as 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain or 4-helical cytokines. You will get no hit for 4-helical cytokine because of the missing s at the end. So, if you do not know the SCOP description exactly use wildcards such as %transglycosylase% or %helical% or %cytokine%.
    Comment search:
    If you are interested in all protein domains complexed with Mg, you can use the search string %complexed with% Mg% and the comments only option selected. The % wildcard after with ensures that you will get a hit, even if the corresponding comment line includes several ligands with Mg not mentioned in the first place.

    protein domain, family, superfamily, fold, class
    comment only
  • Search for PDB entries via Gene Ontology terms
    The search for the GO term electron transporter returns all GO term names for which electron transporter is part of the name or of the description.
    The search for the GO accession number GO:0005489 returns only the term (electron transporter acitivity in this case) that is directly assigned to this number.
  • The GO2PDB mapping is done by combining the SWISS-PROT/PDB cross reference scheme of the IMB Jena Image Library and the mapping of SWISS-PROT KEYWORDS to GO terms provided by SWISS-PROT.
    It does not cover all PDB protein entries.
  • Search for PDB entries via the NCBI species name
    Bacillus anthracis OR lus anthra OR B% anthra OR ant_racis
    will all lead to Bacillus anthracis PDB entries (as does anthrax ).
    So, both common names and (alternative) scientifc species names can be used.
    It is not possible to search for genus names.
  • Browse the NCBI-based Genus/Species Classification.

    This classification combines information from NCBI, SWISS-PROT and PDB and yields more comprehensive results as the SWISS-PROT based species search. 


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