Sequence     &     Structural     Information
	
PTM
PTM N-linked Glycosylation
Sequence Information
Uniprot AC P11609
Organism MOUSE (Mouse)
Modified Amino Acid N(Asn) 60
Annotation dbPTM details N-linked (GlcNAc...).
Structure Information
PDB ID Code 3SDA
Model -
Chain A
Position 42
SCOP Class None
MODRES GLYCOSYLATION SITE
Related PTM
Found in same PDB Chain 20 165
Found in same Uniprot AC
Sort by: PDB ID Code (idpdb-chain_aa) Sequence position (aa_idpdb-chain)
1Z5L-A_N38 1Z5L-A_N60 1Z5L-A_N183 1Z5L-C_N60 1Z5L-C_N183 1ZHN-A_N38 1ZHN-A_N60 1ZHN-A_N183 2AKR-A_N38 2AKR-A_N60 2AKR-A_N183 2AKR-C_N38 2AKR-C_N60 2AKR-C_N183 2FIK-A_N38 2FIK-A_N60 2FIK-A_N183 2GAZ-A_N38 2GAZ-A_N60 2GAZ-A_N183 2Q7Y-A_N38 2Q7Y-A_N60 2Q7Y-A_N183 2Q7Y-C_N38 2Q7Y-C_N60 2Q7Y-C_N183 3ARB-A_N38 3ARB-A_N60 3ARB-A_N183 3ARD-A_N38 3ARD-A_N60 3ARD-A_N183 3ARE-A_N38 3ARE-A_N60 3ARE-A_N183 3ARF-A_N38 3ARF-A_N60 3ARF-A_N183 3ARG-A_N38 3ARG-A_N60 3ARG-A_N183 3AU1-A_N38 3AU1-A_N60 3AU1-A_N183 3G08-A_N38 3G08-A_N60 3G08-A_N183 3GML-A_N38 3GML-A_N60 3GML-A_N183 3GMM-A_N38 3GMM-A_N60 3GMM-A_N183 3GMN-A_N38 3GMN-A_N60 3GMN-A_N183 3GMO-A_N38 3GMO-A_N60 3GMO-A_N183 3GMP-A_N38 3GMP-A_N60 3GMP-A_N183 3GMQ-A_N38 3GMQ-A_N60 3GMQ-A_N183 3GMR-A_N38 3GMR-A_N60 3GMR-A_N183 3HE6-A_N38 3HE6-A_N60 3HE6-A_N183 3HE7-A_N38 3HE7-A_N60 3HE7-A_N183 3ILP-A_N183 3ILQ-C_N38 3ILQ-C_N60 3ILQ-C_N183 3MA7-A_N60 3MA7-A_N183 3MA7-C_N60 3MA7-C_N183 3O8X-A_N38 3O8X-A_N60 3O8X-A_N183 3O9W-A_N38 3O9W-A_N60 3O9W-A_N183 3QI9-A_N38 3QI9-A_N60 3QI9-A_N183 3QUX-A_N38 3QUX-A_N60 3QUX-A_N183 3QUY-A_N38 3QUY-A_N60 3QUY-A_N183 3QUZ-A_N38 3QUZ-A_N60 3QUZ-A_N183 3RTQ-A_N38 3RTQ-A_N60 3RTQ-A_N183 3RUG-A_N38 3RUG-A_N60 3RUG-A_N183 3RUG-C_N38 3RUG-C_N60 3RUG-C_N183 3RZC-A_N38 3RZC-A_N60 3RZC-A_N183 3SCM-A_N38 3SCM-A_N60 3SCM-A_N183 3SDA-A_N38 3SDA-A_N183 3SDC-A_N38 3SDC-A_N60 3SDC-A_N183 3SDD-A_N38 3SDD-A_N60 3SDD-A_N183 3T1F-A_N38 3T1F-A_N60 3T1F-A_N183 3TA3-A_N38 3TA3-A_N60 3TA3-A_N183 3TN0-A_N38 3TN0-A_N60 3TN0-A_N183 3TO4-A_N38 3TO4-A_N60 3TO4-A_N183 3TVM-A_N38 3TVM-A_N60 3TVM-A_N183 3TVM-E_N38 3TVM-E_N60 3TVM-E_N183 3UBX-A_N60 3UBX-A_N183 3UBX-D_N60 3UBX-D_N183 4EI5-A_N38 4EI5-A_N60 4EI5-A_N183 4EI5-E_N38 4EI5-E_N60 4EI5-E_N183 4ELM-A_N38 4ELM-A_N60 4ELM-A_N183 4ELM-C_N38 4ELM-C_N60 4ELM-C_N183 4IRJ-A_N38 4IRJ-A_N60 4IRJ-A_N183 4IRS-A_N38 4IRS-A_N60 4IRS-A_N183 4MX7-A_N38 4MX7-A_N60 4MX7-A_N183
N38_1Z5L-A N38_1ZHN-A N38_2AKR-A N38_2AKR-C N38_2FIK-A N38_2GAZ-A N38_2Q7Y-A N38_2Q7Y-C N38_3ARB-A N38_3ARD-A N38_3ARE-A N38_3ARF-A N38_3ARG-A N38_3AU1-A N38_3G08-A N38_3GML-A N38_3GMM-A N38_3GMN-A N38_3GMO-A N38_3GMP-A N38_3GMQ-A N38_3GMR-A N38_3HE6-A N38_3HE7-A N38_3ILQ-C N38_3O8X-A N38_3O9W-A N38_3QI9-A N38_3QUX-A N38_3QUY-A N38_3QUZ-A N38_3RTQ-A N38_3RUG-A N38_3RUG-C N38_3RZC-A N38_3SCM-A N38_3SDA-A N38_3SDC-A N38_3SDD-A N38_3T1F-A N38_3TA3-A N38_3TN0-A N38_3TO4-A N38_3TVM-A N38_3TVM-E N38_4EI5-A N38_4EI5-E N38_4ELM-A N38_4ELM-C N38_4IRJ-A N38_4IRS-A N38_4MX7-A N60_1Z5L-A N60_1Z5L-C N60_1ZHN-A N60_2AKR-A N60_2AKR-C N60_2FIK-A N60_2GAZ-A N60_2Q7Y-A N60_2Q7Y-C N60_3ARB-A N60_3ARD-A N60_3ARE-A N60_3ARF-A N60_3ARG-A N60_3AU1-A N60_3G08-A N60_3GML-A N60_3GMM-A N60_3GMN-A N60_3GMO-A N60_3GMP-A N60_3GMQ-A N60_3GMR-A N60_3HE6-A N60_3HE7-A N60_3ILQ-C N60_3MA7-A N60_3MA7-C N60_3O8X-A N60_3O9W-A N60_3QI9-A N60_3QUX-A N60_3QUY-A N60_3QUZ-A N60_3RTQ-A N60_3RUG-A N60_3RUG-C N60_3RZC-A N60_3SCM-A N60_3SDC-A N60_3SDD-A N60_3T1F-A N60_3TA3-A N60_3TN0-A N60_3TO4-A N60_3TVM-A N60_3TVM-E N60_3UBX-A N60_3UBX-D N60_4EI5-A N60_4EI5-E N60_4ELM-A N60_4ELM-C N60_4IRJ-A N60_4IRS-A N60_4MX7-A N183_1Z5L-A N183_1Z5L-C N183_1ZHN-A N183_2AKR-A N183_2AKR-C N183_2FIK-A N183_2GAZ-A N183_2Q7Y-A N183_2Q7Y-C N183_3ARB-A N183_3ARD-A N183_3ARE-A N183_3ARF-A N183_3ARG-A N183_3AU1-A N183_3G08-A N183_3GML-A N183_3GMM-A N183_3GMN-A N183_3GMO-A N183_3GMP-A N183_3GMQ-A N183_3GMR-A N183_3HE6-A N183_3HE7-A N183_3ILP-A N183_3ILQ-C N183_3MA7-A N183_3MA7-C N183_3O8X-A N183_3O9W-A N183_3QI9-A N183_3QUX-A N183_3QUY-A N183_3QUZ-A N183_3RTQ-A N183_3RUG-A N183_3RUG-C N183_3RZC-A N183_3SCM-A N183_3SDA-A N183_3SDC-A N183_3SDD-A N183_3T1F-A N183_3TA3-A N183_3TN0-A N183_3TO4-A N183_3TVM-A N183_3TVM-E N183_3UBX-A N183_3UBX-D N183_4EI5-A N183_4EI5-E N183_4ELM-A N183_4ELM-C N183_4IRJ-A N183_4IRS-A N183_4MX7-A
Gallery (?)
Slide 1
Slide 2
Example Frame



Note: As the images production is automatic, the focus on the PTM site could not be the most optimized.
      In these cases it is recommended to use the PyMOL script to visualize the PTM site in 3D.
Alignment
(?)

	           Numerotation

	(?)       Uniprot Sequence
	(?)                Clustal
	(?)           PDB Sequence
	(?)        PDB Information
	(?)          DSSP Sequence
	(?) Protein Block Sequence
	
         1         2         3         4         5         6         7         8         9         10        11        12        13        14        15        16        17        18        19        20        21        22        23        24        25        26        27        28        29        30        31        32        33        
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MRYLPWLLLWAFLQVWGQSEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSADGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWDARQAPVGLIVFIVLIMLVVVGAVVYYIWRRRSAYQDIR
                  ********************************************************************************************************************************************************************************************************.******************************************************************************.:               *  :  .   :*.:*  ::.  
------------------SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGS---------------LHHILDAQKMVWNHRHHHHHH-
                  MMMMM___________________________________________________________________________________________________________________________________________________________________________________________________S______________________________________________________________________________SS               SSSSSSSSSSSSSSMMMMMMM 
                       CCCBEEEEEEEEECSSSCEEEEEEEEETTEEEEEECTTCSSCEESSTTTTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCSCEEEEEEEEEEEETTTEEEEEEEEEETTEEEEEEETTEEEECTTCCGGGHHHHHHHHTCHHHHHHHHHHHHTHHHHHHHHHHHHTHHHHTCCBCCEEEEEEEECSSTTEEEEEEEEEEEBSSCCEEEEEETTEECTTCEECCCEECTTSCEEEEEEEEEETTCCTTEEEEEECTTTTTCCEEEETTC               HHHHHHHHTTCCCC        
                       ZZadddddddddfblmlccddddddehjbcfbdcdfklmbdcdfbfklnmmacfklmmmmmmmmmmmmmmmmmmmmmmmmmnmmmpccdddddddddddddddddddddddddeehiafbdcehjaccddehiafklmmmmmmmmmmmmlmmmmmmmmmmmmmmmmmmmmmmmmmmmmgccdddddddddddfbghiacdddddehiacfbdcddddehjbccfkbccddddddfkopacddddddddehilgopacddddfklmmmccdddehia               klmmmmmmmgccZZ        

Scripts     (PyMol,     Modeller,     ...)

PyMol
	Download
Modeller
	
If you want to use this structure as a template for modelisation with Modeller, you can use the following sequence to build the alignment file "*.ali".

To avoid the classical Modeller error :

			'Number of residues in the alignment and pdb files are different'(see FAQ n°17),

the missing residues, non-classical amino-acids, and sequence gaps have been replaced by a "X" symbol.
			
XXXXXKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHXXXXXXX
1) align this sequence with your sequence to modelised;
2) replace the "X" by "-" in the obtained alignement, then build your "*.ali" file;
3) use Modeller to make your models;
4) And finally use the following information found in the PDB to add this PTM in your models (see FAQ n°8 & 9 and this archive of Modeller usage).
			
REMARK 500 ND2 ASN A 42 O5 NAG A 304 1.73
MODRES 3SDA ASN A 42 ASN GLYCOSYLATION SITE
LINK ND2 ASN A 42 C1 NAG A 304 1555 1555 1.35
ATOM 308 N ASN A 42 2.695 -98.153 -36.560 1.00 49.52 N
ATOM 309 CA ASN A 42 1.946 -96.937 -36.773 1.00 49.87 C
ATOM 310 C ASN A 42 2.750 -95.755 -36.377 1.00 50.27 C
ATOM 311 O ASN A 42 2.637 -94.708 -36.946 1.00 50.33 O
ATOM 312 CB ASN A 42 0.687 -96.921 -35.918 1.00 49.80 C
ATOM 313 CG ASN A 42 -0.204 -95.745 -36.204 1.00 49.59 C
ATOM 314 OD1 ASN A 42 -1.140 -95.863 -36.931 1.00 49.00 O
ATOM 315 ND2 ASN A 42 0.079 -94.621 -35.621 1.00 49.25 N
HETATM 6605 C1 NAG A 304 -0.858 -93.715 -35.265 1.00 66.88 C
HETATM 6606 C2 NAG A 304 -1.273 -92.956 -34.016 1.00 66.75 C
HETATM 6607 C3 NAG A 304 -2.101 -91.779 -34.509 1.00 67.12 C
HETATM 6608 C4 NAG A 304 -1.189 -90.907 -35.373 1.00 67.37 C
HETATM 6609 C5 NAG A 304 -0.406 -91.708 -36.426 1.00 67.17 C
HETATM 6610 C6 NAG A 304 0.735 -90.884 -37.019 1.00 67.33 C
HETATM 6611 C7 NAG A 304 -1.232 -94.499 -32.149 1.00 65.36 C
HETATM 6612 C8 NAG A 304 -2.011 -95.379 -31.224 1.00 65.62 C
HETATM 6613 N2 NAG A 304 -1.935 -93.832 -33.067 1.00 65.92 N
HETATM 6614 O3 NAG A 304 -2.609 -91.019 -33.439 1.00 67.37 O
HETATM 6615 O4 NAG A 304 -1.972 -89.948 -36.031 1.00 68.00 O
HETATM 6616 O5 NAG A 304 0.120 -92.914 -35.898 1.00 66.85 O
HETATM 6617 O6 NAG A 304 1.695 -90.579 -36.030 1.00 67.81 O
HETATM 6618 O7 NAG A 304 -0.010 -94.426 -32.026 1.00 64.49 O