©CMBI 2008 Databases Data must be in a certain format for software to recognize Every database can have its own format but some data elements are essential for every database: 1. Unique identifier, or accession code 2. Name of depositor 3. Literature references 4. Deposition date 5. The real data

©CMBI 2008 Quality of Data SwissProt Data is only entered by annotation experts EMBL, PDB “Everybody” can submit data No human intervention when submitted; some automatic checks

©CMBI 2008 SwissProt database Database of protein sequences entries (Oct 2008) Ca. 200 Annotation experts worldwide Keyword-organised flatfile Obligatory deposit of in SwissProt before publication Presently, databases are being merged into UniProt.

©CMBI 2008 Important records in SwissProt (1) ID HBA_HUMAN Reviewed; 142 AA. AC P69905; P01922; Q3MIF5; Q96KF1; Q9NYR7; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 2. DT 23-SEP-2008, entry version 63. DE RecName: Full=Hemoglobin subunit alpha; DE AltName: Full=Hemoglobin alpha chain; DE AltName: Full=Alpha-globin;

©CMBI 2008 Important records in SwissProt (2) Cross references section: Hyperlinks to all entries in other databases which are relevant for the protein sequence HBA_HUMAN

©CMBI 2008 Important records in SwissProt (3) Features section: post-translational modifications, signal peptides, binding sites, enzyme active sites, domains, disulfide bridges, local secondary structure, sequence conflicts between references etc. etc.

©CMBI 2008 And finally, the amino acid sequence!

©CMBI 2008 Protein Data Bank (PDB) Databank for macromolecular structure data (3-dimensional coordinates). Started ca. 30 years ago (on punched cards!) Obligatory deposit of coordinates in the PDB before publication ~ entries (April 2008) ( ~2500 “unique” structures) PDB file is a keyword-organised flat-file (80 column) 1) human readable 2) every line starts with a keyword (3-6 letters) 3) platform independent

©CMBI 2008 PDB important records (1) PDB nomenclature Filename= accession number= PDB Code Filename is 4 positions (often 1 digit & 3 letters, e.g. 1CRN) HEADER describes molecule & gives deposition date HEADER PLANT SEED PROTEIN 30-APR-81 1CRN CMPND name of molecule COMPND CRAMBIN SOURCE organism SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED

©CMBI 2008 PDB important records (2) SEQRES Sequence of protein; be aware: Not always all 3d-coordinates are present for all the amino acids in SEQRES!! SEQRES 1 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE 1CRN 51 SEQRES 2 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS 1CRN 52 SEQRES 3 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR 1CRN 53 SEQRES 4 46 CYS PRO GLY ASP TYR ALA ASN 1CRN 54 SSBOND disulfide bridges SSBOND 1 CYS 3 CYS 40 SSBOND 2 CYS 4 CYS 32

©CMBI 2008 PDB important records (3) and at the end of the PDB file the “real” data: ATOM one line for each atom with its unique name and its x,y,z coordinates ATOM 1 N THR CRN 70 ATOM 2 CA THR CRN 71 ATOM 3 C THR CRN 72 ATOM 4 O THR CRN 73 ATOM 5 CB THR CRN 74 ATOM 6 OG1 THR CRN 75 ATOM 7 CG2 THR CRN 76 ATOM 8 N THR CRN 77 ATOM 9 CA THR CRN 78 ATOM 10 C THR CRN 79 ATOM 11 O THR CRN 80

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