Sequence     &     Structural     Information
	
PTM
PTM N-linked Glycosylation
Sequence Information
Uniprot AC P21836
Organism MOUSE (Mouse)
Modified Amino Acid N(Asn) 495
Annotation dbPTM details N-linked (GlcNAc...).
Structure Information
PDB ID Code 2GYW
Model -
Chain A
Position 464
SCOP Class c (Alpha and beta proteins (a/b))
MODRES GLYCOSYLATION SITE
Related PTM
Found in same PDB Chain 350
Found in same Uniprot AC
Sort by: PDB ID Code (idpdb-chain_aa) Sequence position (aa_idpdb-chain)
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
	
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MRPPWYPLHTPSLAFPLLFLLLSLLGGGARAEGREDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWSGVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPVLIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNVGLLDQRLALQWVQENIAAFGGDPMSVTLFGESAGAASVGMHILSLPSRSLFHRAVLQSGTPNGPWATVSAGEARRRATLLARLVGCPPGGAGGNDTELIACLRTRPAQDLVDHEWHVLPQESIFRFSFVPVVDGDFLSDTPEALINTGDFQDLQVLVGVVKDEGSYFLVYGVPGFSKDNESLISRAQFLAGVRIGVPQASDLAAEAVVLHYTDWLHPEDPTHLRDAMSAVVGDHNVVCPVAQLAGRLAAQGARVYAYIFEHRASTLTWPLWMGVPHGYEIEFIFGLPLDPSLNYTTEERIFAQRLMKYWTNFARTGDPNDPRDSKSPQWPPYTTAAQQYVSLNLKPLEVRRGLRAQTCAFWNRFLPKLLSATDTLDEAERQWKAEFHRWSSYMVHWKNQFDHYSKQERCSDL
                               ***************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************                                        
-------------------------------EGREDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWSGVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPVLIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNVGLLDQRLALQWVQENIAAFGGDPMSVTLFGESAGAASVGMHILSLPSRSLFHRAVLQSGTPNGPWATVSAGEARRRATLLARLVGCPPGGAGGNDTELIACLRTRPAQDLVDHEWHVLPQESIFRFSFVPVVDGDFLSDTPEALINTGDFQDLQVLVGVVKDEGSYFLVYGVPGFSKDNESLISRAQFLAGVRIGVPQASDLAAEAVVLHYTDWLHPEDPTHLRDAMSAVVGDHNVVCPVAQLAGRLAAQGARVYAYIFEHRASTLTWPLWMGVPHGYEIEFIFGLPLDPSLNYTTEERIFAQRLMKYWTNFARTGDPNDPRDSKSPQWPPYTTAAQQYVSLNLKPLEVRRGLRAQTCAFWNRFLPKLLSAT----------------------------------------
                               _________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________MMMMMMM______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________M                                        
                               CCSSCGGGEEEETTEEEECEEEEETTEEEEEEEEEECBCCCCGGGTTSCCCBCCCCSSEEECBSCCCEESCCCCCSSTTCHHHHTTSCCSCEESCCCEEEEEEESSCCSSCEEEEEEECCSTTTCCCTTSGGGCTHHHHHHHCCEEEEECCCCHHHHHCCCTTCSSCCSCHHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHCHHHHTTCSEEEEESCCSSSSSSCBCHHHHHHHHHHHHHHTTC       CHHHHHHHHHTSCHHHHHHHHGGGCSSSCSSCCSSCCBCCSSSSSSCHHHHHHHCCCTTCEEEEEEETBTTHHHHTTTCTTCCTTSCCCCCHHHHHHHHHHHSTTCCHHHHHHHHHHHSCTTSTTCHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTTCEEEEEEECCCCTTCCSCGGGCSBTTTTHHHHTTGGGSGGGCCCHHHHHHHHHHHHHHHHHHHHSCCSCSSCCSSCCCCCCCTTTCEEEEESSSCCEEEECSSHHHHHHHHHTHHHHHCC                                         
                               ZZmcfklgccdfkbccdddddddfkbccdddehiafbdcfehjlgoiacddddddehjddffbccddddddddfklgoiaklmmmpccbdcdfblcccdddddddddfbacdddddddehehpgccfkbfklocklmmmmnopacddddddehjllmoccehiaklngjklmmmmmmmmmmmmmmmmmnopafklccdddehjlmmmmmmmmmpmklmmmcfbdcdehiafedjklpccfklmmmmmmmmmmmnoZZ       ZZlmmmmmmmpcfklmmmmmmmmcfbdcehiafbdcddehlmpmbdfklmmmmmccklaccdddddfblmlmmmmnopghiafkbgoiacfklmmmmmmmmmmmbcfklmmmmmmmmpcfklmmbmklmmmmmmmmmmmmmmmmmmmmmmmmmmmnopacdddddfbdcfkbcbdfklopaehilmmmmnommmmmknopafklmmmmmmmmmmmmmmmmnopabdfklmmbccdddddfklopacdddfbdcdddehjhklmmmmmmmmmmmmmnZZ                                         

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.
			
EGREDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWSGVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPVLIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNVGLLDQRLALQWVQENIAAFGGDPMSVTLFGESAGAASVGMHILSLPSRSLFHRAVLQSGTPNGPWATVSAGEARRRATLLARLVGCXXXXXXXNDTELIACLRTRPAQDLVDHEWHVLPQESIFRFSFVPVVDGDFLSDTPEALINTGDFQDLQVLVGVVKDEGSYFLVYGVPGFSKDNESLISRAQFLAGVRIGVPQASDLAAEAVVLHYTDWLHPEDPTHLRDAMSAVVGDHNVVCPVAQLAGRLAAQGARVYAYIFEHRASTLTWPLWMGVPHGYEIEFIFGLPLDPSLNYTTEERIFAQRLMKYWTNFARTGDPNDPRDSKSPQWPPYTTAAQQYVSLNLKPLEVRRGLRAQTCAFWNRFLPKLLSAX
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).
			
MODRES 2GYW ASN A 464 ASN GLYCOSYLATION SITE
HELIX 23 23 GLY A 456 ASN A 464 5 9
LINK ND2 ASN A 464 C1 NAG A 701 1555 1555 1.45
ATOM 3523 N ASN A 464 11.093 28.879 25.339 1.00 48.96 N
ATOM 3524 CA ASN A 464 10.246 29.475 24.277 1.00 49.39 C
ATOM 3525 C ASN A 464 9.740 28.556 23.152 1.00 47.81 C
ATOM 3526 O ASN A 464 9.332 29.048 22.096 1.00 47.67 O
ATOM 3527 CB ASN A 464 10.919 30.717 23.644 1.00 50.32 C
ATOM 3528 CG ASN A 464 11.051 31.877 24.616 1.00 55.43 C
ATOM 3529 OD1 ASN A 464 10.385 31.916 25.658 1.00 54.65 O
ATOM 3530 ND2 ASN A 464 11.922 32.839 24.270 1.00 64.31 N
HETATM 8363 C1 NAG A 701 12.136 33.799 25.335 1.00 74.10 C
HETATM 8364 C2 NAG A 701 13.509 34.518 25.350 1.00 78.87 C
HETATM 8365 C3 NAG A 701 13.570 35.793 26.224 1.00 80.03 C
HETATM 8366 C4 NAG A 701 12.233 36.563 26.235 1.00 80.55 C
HETATM 8367 C5 NAG A 701 11.144 35.551 26.647 1.00 80.14 C
HETATM 8368 C6 NAG A 701 9.789 36.122 27.117 1.00 81.08 C
HETATM 8369 C7 NAG A 701 15.244 32.810 24.911 1.00 79.55 C
HETATM 8370 C8 NAG A 701 15.737 31.477 25.406 1.00 79.34 C
HETATM 8371 N2 NAG A 701 14.563 33.584 25.767 1.00 79.11 N
HETATM 8372 O3 NAG A 701 14.652 36.617 25.817 1.00 79.92 O
HETATM 8373 O4 NAG A 701 12.296 37.697 27.085 1.00 81.36 O
HETATM 8374 O5 NAG A 701 10.999 34.639 25.559 1.00 77.74 O
HETATM 8375 O6 NAG A 701 9.130 36.898 26.134 1.00 80.94 O
HETATM 8376 O7 NAG A 701 15.481 33.146 23.751 1.00 80.13 O