pdb2linucs options
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Find carbohydrates in HETATM only / ATOM only / ATOM and HETATM:
Standard pdb-files distinguish between protein / nucleic acid atoms (stored in ATOM records) and other atoms (stored in HETATM records). Therefore, carbohydrate information is normally only found in HETATM records. To increase efficiency, pdb2linucs only searches for carbohydrate rings in the HETATM records. If you are using non-standard pdb-files, you might want to search also (or only) in ATOM records which you can force by changing this option. -
Assign connections by atom distances
In standard pdb-files connectivities for atoms stored in HETATM records should be given explicitely in the CONECT records. Consequently it should not be necessary to determine connectivities by atom distances.
In some files there are overlapping residues (e.g. if the cristal was soaked with a mixture of α and β carbohydrate, in some unit cells there will be the further and in others the latter form, which results in an overlapping of both forms in the total data). In this case the distance-based determination of connectivities will probably lead to errors.
In other files some connectivities are missing. Then you can force pdb2linucs to calculate them by switching on this option. Again, you have the choise between calculating connectivities for HETATM records only, ATOM records only or both types of records. -
Structure viewer / Viewer size
Structures can be visualised using the java applet Jmol or the Chime plugin. Chime is available for Windows and Mac, on Linux computers it can be used together with the crossover plugin.
You can adjust the size of the applet/plugin to your screen size. -
Residue colors
The detected carbohydrates can be coloured by chain type, i.e. distinction between N-glycans, O-glycans and non-glycosidically bound ligands, or by residue type. If you switch off colouring, the ligands will be in the standard cpk colours. -
Phosphate handling
Phosphate groups are handled by pdb2linucs either as single residues or as substituents.
The resulting Linucs-Codes for a b-D-Fructose-2,6-bisphosphate monosaccharide, for example, are [][P]{[(0+2)][b-D-Fruf]{[(6+0)][P]{}}} for the single residue mode or [][b-D-FrufPO36PO3]{} for the substituent mode, respectively.
In GlycoSciencesDB, phosphate groups are treated as single residues, therefore a direct link to the database can only be offered in that mode. -
Notation
Internally, pdb2linucs works with the LINUCS notation, which is optimised for use in computer software and databases. Since most glycobiologists are more familiar with the IUPAC notation, pdb2linucs offers the possibility to use this nomenclature as output format.
Output description for example 1agm:
PDB entry 1agm is an example for a pdb-file containing carbohydrates as N-glycans, O-glycans and non-covalently bound ligand.As you can see on the results page, this structure of a hydrolase was solved in 1994 at 2.4 angstroms resolution. The experimental method can not be determined from the pdb-file. For further information not available on the results page, you can use the cross-link to the respective PDB entry.
pdb2linucs results for 1agm:
HYDROLASE 13-MAY-94 1AGM 1AGM 2 |
Below this general information, you can view the structure with the Jmol applet or the Chime plugin (if not disabled in the options). The N-linked chains are coloured blue, the O-linked residues red and the non-covalently bound ligand is yellow:
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Beneath that, detailed information about the detected carbohydrates is displayed using the LINUCS code, each line representing one carbohydrate chain. To prevent horizontal scrolling, the first two lines in this example are shortened here.
In case there is a corresponding entry available in GlycosciencesDB, a direct link to that database is established (Button "Explore"). If a chain consists of at least 2 residues, 2 further buttons are available. The first one reveals the structure in IUPAC notation, which is easier to survey for humans than the LINUCS code, especially for branched structures (2nd line in example). The last button leads to a graphical representation of the structure (obtained by LiGraph).
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The last information given in the results for glycoprotein structures is the amino acid sequence of the protein. The residues participating in a glycosylation site are marked blue for N-glycans and red for O-glycans:
1 ATLDSWLSNE ATVARTAILN NIGADGAWVS GADSGIVVAS PSTDNPDYFY TWTRDSGLVI 60 61 KTLVDLFRNG DTDLLSTIEH YISSQAIIQG VSNPSGDLSS GGLGEPKFNV DETAYTGSWG 120 121 RPQRDGPALR ATAMIGFGQW LLDNGYTSAA TEIVWPLVRN DLSYVAQYWN QTGYDLWEEV 180 181 NGSSFFTIAV QHRALVEGSA FATAVGSSCS WCDSQAPQIL CYLQSFWTGS YILANFDSSR 240 241 SGKDTNTLLG SIHTFDPEAG CDDSTFQPCS PRALANHKEV VDSFRSIYTL NDGLSDSEAV 300 301 AVGRYPEDSY YNGNPWFLCT LAAAEQLYDA LYQWDKQGSL EITDVSLDFF KALYSGAATG 360 361 TYSSSSSTYS SIVSAVKTFA DGFVSIVETH AASNGSLSEQ FDKSDGDELS ARDLTWSYAA 420 421 LLTANNRRNS VVPPSWGETS ASSVPGTCAA TSASGTYSSV TVTSWPSIVA 470 |
If the structure contains glycosidic linkages, a direct link to carp for analysis of linkage torsions is provided as well: