Introduction
Query
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Database Description
Terms
Introduction
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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Query
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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Donwload
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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Terms
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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