pdb2linucs options


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
RESOLUTION: 2.4 ANGSTROMS.
EXP. METHOD: not available



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:



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).

display chain in iupac notationgraphical representation of chain[][ASN]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]...
display chain in iupac notationgraphical representation of chain[][ASN]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]...
display chain in iupac notationgraphical representation of chain[][SER]{[(3+1)][a-D-Manp]{}}
display chain in iupac notationgraphical representation of chain[][SER]{[(3+1)][a-D-Manp]{}}
display chain in iupac notationgraphical representation of chain[][THR]{[(3+1)][a-D-Manp]{}}


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:

Analyse linkage torsions for entry 1agm using carp:
Select data source for plot background:
PDB (NMR-like definition)
PDB (crystallographic definition)
GlycoMapsDB
Select graphics type:
GIF
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