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ProtBuD is a comprehensive database of asymmetric units (ASU) and biological units (BU) from PDB and PQS, and uses SCOP and PSIBLAST to provide ASU and BU for all entries with proteins in particular superfamilies or families. A user can search for a particular SCOP designation or a particular entry or chain in an entry and obtain the asymmetric and biological unit content of nearly all (except some non-SCOP or too distantly related new entries) related proteins in the PDB. A user can update the database weekly by adding new entries, updating modified entries and removing obsolete entries instead of rebuilding the whole database. The database also provides the information whether two PDB/PQS biological units of an entry same or not.

When browsing the biological units in a SCOP designation and/or PSI-BLAST homologous groups, a user can download PDB ASU, PDB BU and PQS BU files into the local machine, use Rasmol or other visualization tool to check the ASU or BUs.

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The tool is designed to find biological units of all PDB entries in a specific SCOP classification level. Generally, a user inputs a PDB entry and/or chain id, the database returns all SCOP domains and their SCOP codes for this PDB entry and/or chain. Then the user clicks a SCOP Family or Superfamily, the database returns RCSB and PQS biological units as well as asymmetric units of all PDB entries in that SCOP Family or Superfamily.  To further explore the entities and asymmetric chains of each PDB, the user just clicks a PDB code cell, or uses key UP or DOWN to navigate PDB codes. Thus, a user can quickly go through all PDB entries to find interesting information. 

For those PDB entries not in SCOP, we use PSI BLAST to find homological PDB entry hits. A table named PsiBlastHit contains homological hits for each nonredundant PDB entry. Data are provided by Guoli Wang which is also updated weekly. If SCOP codes are not available for the query PDB entry, the database returns a list  of PDB hits and their corresponding SCOP Codes if exist. A user can check which SCOP classification level is more likely to be the classification the query PDB entry belongs to, then click SCOP codes to study biological units of all PDB entries in the SCOP classification level. 

If there are no PSI BLAST hits in the database, the tool just returns the biological units and asymmetric units of this PDB entry. 

User can directly input a SCOP Family or Superfamily to see biological units of all PDB entries in the SCOP classification. 

(All pictures are taken from the stand-alone tool.)

      1. Enter one SCOP Code or two SCOP codes at Fold or Superfamily or Family level. For example, b.2.5.2 (Family: p53 DNA-binding domain-like). A list of biological units of all PDB entries in the SCOP classification designation is returned by the database. In case of two SCOP codes, all PDB entries contains at least two domains in these two SCOP codes.

Figure 1.

      2. Click any one PDB code cell to display entities and asymmetric chains.  

Figure 2.

      3. Turn on interface check box to display all unique interfaces of the entry biological unit. In order to display interfaces window, a user must turn off Popups blocker for  the web site.

Figure 3.

      1.  Enter PDB code and/or chain ID (entity ID). SCOP domains and SCOP codes of this PDB entry and/or chain are returned by the database.

Figure 4.

      2. Click SCOP code Family or Superfamily or Fold, return biological units of all PDB entries in the SCOP classification. See figure 2.

Figure 5.

       3. A list of PSI-BLAST hits for PDB entry 1pk1. Click Hit Entry cell get the ASU/BU, Entity and asymmetric chains tables. Or click Family, Superfamily or Fold to get the ASU/BU of a list of PDB entries.

Figure 6.

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It is convenient for a user to access the coordinates files from PDB and PQS. When browsing the biological units in a SCOP designation and/or PSI-BLAST homologous groups, a user can download PDB ASU, PDB BU and PQS BU files into the local machine, use Rasmol or other visualization tool to check the ASU or BUs.

1. In the biological unit table, the columns for ASU-ABC, PDBBU-ABC and PQSBU-ABC are hyper link columns. A user can download the file just by right-click the cell text, save the target to local machine.

Figure 7.

2. In the interface table, the columns of PdbInterfaceID and PqsInterfaceID are hyperlink columns. A user can download the interface file by right click then save target to local machine

Figure 8.

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1. Asymmetric Unit: The asymmetric unit is defined as the smallest portion of a crystal structure that has no crystallographic symmetry. A crystal unit cell is generated from the asymmetric unit by applying crystallographic symmetry operations. See PDB Biological Unit Tutorial

2. Biological Unit: A biological unit is a biological functional unit, often revealed in X-ray structures, either as the asymmetric unit itself or in a subset of the asymmetric unit or a superset of asymmetric units.see PDB Biological Unit Tutorial

3. Data String Format

Formats Description Example (1gzh)
Asymmetric Format Unique PDB chains with number of copies (A)(B, D)(C)
Author Chain Format Author-named chains with number of copies (A)(B, D)(C)
Entity Format Entity ID with number of copies (1.1)(2.2)(3.1)
ABC Format ABC chains with number of copies* A2BC
* ABC format only uses the letters A, B, C, ... and begins with A and maximum number of copies. 

    4. Modified Residue Format

     The format of modified residues in Asymmetric Chain table is RCSB sequence number (Author sequence number): standard residue -> modified residue (modification details). (e.g. 18(19): ALA -> AIB (ALPHA-AMINOISOBUTYRIC)). There are 4 other cases:

  • Author sequence number is same as author sequence number, only list RCSB sequence number. e.g. 18: ALA -> AIB (ALPHA-AMINOISOBUTYRIC)
  • Modified residue is same as standard residue, only list standard residue. e.g. 18: ASN (GLYCOSYLATION)
  • No standard residue name. e.g. 18: MLY (N-DIMETHYL-LYSINE)
  • No RCSB residue number but there is author residue number. (19): ASM (2-AMINO-4-OXO-4(1H-PYRROL-1-YL)BUTANOIC ACID).

    5. Covalent Attachments

    Covalent attachments of an asymmetric chain is a list of asymmetric chains that are covalently attached. For instance, if "A" is a polypeptide and "K" is a Zinc, then on the covalent asymmetric chains for "A" there will be "K" in the covalent attachment list, and "A" will be listed in the list for "K". 

    6. Missing Residues In Coordinates

    Residues are missed in RCSB sequence. 

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