Description
Returns the PDB and chain IDs of the provided protein
Usage
uniprot2pdb(up_id)
Arguments
up_id the UniProt ID.
Value
The function returns a dataframe with info about the PDB related to the protein of interest.
See Also
pdb2uniprot(), id.mapping()
Details
The ptm package contains a number of ancillary functions that deal with Protein Data Bank (PDB) files. These functions may be useful when structural 3D data need to be analyzed. The mentioned functions are:
- uniprot2pdb (the current document)
- pdb2uniprot
- pdb.chain
- pdb.quaternary
- pdb.res
- pdb.pep
- pdb.select
- compute.dssp
- parse.dssp
- mkdssp
One of the most basic operations consists of interconversion between identifiers. For instance, suppose we have a the human hemoglobin subunit alpha (P69905), and we want to explore the PDB files where this subunit appears:
pdbs <- uniprot2pdb('P69905')
The dataframe we have called pdbs contains 534 observations, but let’s take a look at some of them.
kable(head(pdbs))
| PDB | CHAIN | SP_PRIMARY | RES_BEG | RES_END | PDB_BEG | PDB_END | SP_BEG | SP_END | |
|---|---|---|---|---|---|---|---|---|---|
| 168 | 1a00 | A | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
| 170 | 1a00 | C | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
| 172 | 1a01 | A | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
| 174 | 1a01 | C | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
| 247 | 1a0u | A | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
| 249 | 1a0u | C | P69905 | 1 | 141 | 1 | 141 | 2 | 142 |
If we don’t care about the chains, and all we want is the PDB IDs where this protein appers, we can proceed as follows:
id.mapping('P69905', from = 'uniprot', to = 'pdb')
## [1] "1A00" "1A01" "1A0U" "1A0Z" "1A3N" "1A3O" "1A9W" "1ABW" "1ABY" "1AJ9" "1B86" "1BAB" "1BBB" "1BIJ" ## [15] "1BUW" "1BZ0" "1BZ1" "1BZZ" "1C7B" "1C7C" "1C7D" "1CLS" "1CMY" "1COH" "1DKE" "1DXT" "1DXU" "1DXV" ## [29] "1FDH" "1FN3" "1G9V" "1GBU" "1GBV" "1GLI" "1GZX" "1HAB" "1HAC" "1HBA" "1HBB" "1HBS" "1HCO" "1HDB" ## [43] "1HGA" "1HGB" "1HGC" "1HHO" "1IRD" "1J3Y" "1J3Z" "1J40" "1J41" "1J7S" "1J7W" "1J7Y" "1JY7" "1K0Y" ## [57] "1K1K" "1KD2" "1LFL" "1LFQ" "1LFT" "1LFV" "1LFY" "1LFZ" "1LJW" "1M9P" "1MKO" "1NEJ" "1NIH" "1NQP" ## [71] "1O1I" "1O1J" "1O1K" "1O1L" "1O1M" "1O1N" "1O1O" "1O1P" "1QI8" "1QSH" "1QSI" "1QXD" "1QXE" "1R1X" ## [85] "1R1Y" "1RPS" "1RQ3" "1RQ4" "1RQA" "1RVW" "1SDK" "1SDL" "1SHR" "1SI4" "1THB" "1UIW" "1VWT" "1XXT" ## [99] "1XY0" "1XYE" "1XZ2" "1XZ4" "1XZ5" "1XZ7" "1XZU" "1XZV" "1Y01" "1Y09" "1Y0A" "1Y0C" "1Y0D" "1Y0T" ## [113] "1Y0W" "1Y22" "1Y2Z" "1Y31" "1Y35" "1Y45" "1Y46" "1Y4B" "1Y4F" "1Y4G" "1Y4P" "1Y4Q" "1Y4R" "1Y4V" ## [127] "1Y5F" "1Y5J" "1Y5K" "1Y7C" "1Y7D" "1Y7G" "1Y7Z" "1Y83" "1Y85" "1Y8W" "1YDZ" "1YE0" "1YE1" "1YE2" ## [141] "1YEN" "1YEO" "1YEQ" "1YEU" "1YEV" "1YFF" "1YG5" "1YGD" "1YGF" "1YH9" "1YHE" "1YHR" "1YIE" "1YIH" ## [155] "1YVQ" "1YVT" "1YZI" "1Z8U" "2D5Z" "2D60" "2DN1" "2DN2" "2DN3" "2DXM" "2H35" "2HBC" "2HBD" "2HBE" ## [169] "2HBF" "2HBS" "2HCO" "2HHB" "2HHD" "2HHE" "2M6Z" "2W6V" "2W72" "2YRS" "3B75" "3D17" "3D7O" "3DUT" ## [183] "3HHB" "3HXN" "3IA3" "3IC0" "3IC2" "3KMF" "3NL7" "3NMM" "3ODQ" "3ONZ" "3OO4" "3OO5" "3OVU" "3P5Q" ## [197] "3QJB" "3QJC" "3QJD" "3QJE" "3R5I" "3S48" "3S65" "3S66" "3SZK" "3WCP" "3WHM" "4FC3" "4HHB" "4IJ2" ## [211] "4L7Y" "4M4A" "4M4B" "4MQC" "4MQG" "4MQH" "4MQI" "4MQJ" "4MQK" "4N7N" "4N7O" "4N7P" "4N8T" "4NI0" ## [225] "4NI1" "4ROL" "4ROM" "4WJG" "4X0L" "4XS0" "5E29" "5E6E" "5E83" "5EE4" "5HU6" "5HY8" "5JDO" "5KDQ" ## [239] "5KSI" "5KSJ" "5NI1" "5SW7" "5U3I" "5UCU" "5UFJ" "5URC" "5VMM" "5WOG" "5WOH" "5X2R" "5X2S" "5X2T" ## [253] "5X2U" "6BB5" "6BNR" "6BWP" "6BWU" "6DI4" "6HAL" "6HBW" "6HK2" "6NBC" "6NBD"
ptm 