1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Live, D. Borgert, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C8 H15 N O6 221.208 2-acetamido-2-deoxy-alpha-D-galactopyranose N-acetyl-alpha-D-galactosamine; 2-acetamido-2-deoxy-alpha-D-galactose; 2-acetamido-2-deoxy-D-galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE D-saccharide, alpha linking C2 H4 O 44.053 ACETYL GROUP non-polymer C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking UK Glycobiology 9999 1460-2423 31 649 661 10.1093/glycob/cwaa112 33295623 Contrasting the conformational effects of alpha-O-GalNAc and alpha-O-Man glycan protein modifications and their impact on the mucin-like region of alpha-dystroglycan. 2021 0000-0003-2187-6872 10.2210/pdb2mk7/pdb pdb_00002mk7 996.180 Alpha-dystroglycan mucin domain peptide (UNP residues 419-427) 1 syn polymer 221.208 2-acetamido-2-deoxy-alpha-D-galactopyranose 4 syn non-polymer Alpha-DG, aDG no yes (ACE)PPTTTTKKP(NH2) XPPTTTTKKPX A polypeptide(L) n n n n n n n n n n n Effects of O-GalNAc glycosylation on structure atom_site chem_comp entity pdbx_chem_comp_identifier pdbx_entity_nonpoly struct_conn struct_ref_seq_dif struct_site struct_site_gen chem_comp citation citation_author database_2 pdbx_database_status repository Initial release Carbohydrate remediation repository Remediation Atomic model Data collection Database references Derived calculations Structure summary Database references Structure summary Other 1 0 2015-02-04 2 0 2020-07-29 2 1 2022-08-24 2 2 2023-06-14 _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp.name _chem_comp.type _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_role _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _chem_comp.pdbx_synonyms _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data DGalpNAca N-acetyl-a-D-galactopyranosamine a-D-GalpNAc GalNAc BMRB Y RCSB 2014-02-02 REL REL REL REL A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose 9606 human Homo sapiens sample structures with the least restraint violations 50 16 2D 1H-1H NOESY 3D TOCSY-NOESY 2D 1H-15N HSQC 2D 1H-13C HSQC 2D 1H-1H TOCSY 2D 1H-1H COSY 2D 1H-13C HMBC 2-10 mM 2-10 mM 4.5 ambient 288 K simulated annealing 1 closest to the average 2-10 mM aDG mucin domain peptide, 100% D2O 100% D2O 2-10 mM aDG mucin domain peptide, 95% H2O/5% D2O 95% H2O/5% D2O Brunger A. T. et.al. refinement XPLOR-NIH 600 Varian INOVA Varian INOVA 800 Varian INOVA Varian INOVA 900 Varian INOVA Varian INOVA A2G 12 2 A2G A2G 101 A A2G 13 2 A2G A2G 102 A A2G 14 2 A2G A2G 103 A A2G 15 2 A2G A2G 104 A ACE 1 n 1 ACE 1 A PRO 2 n 2 PRO 2 A PRO 3 n 3 PRO 3 A THR 4 n 4 THR 4 A THR 5 n 5 THR 5 A THR 6 n 6 THR 6 A THR 7 n 7 THR 7 A LYS 8 n 8 LYS 8 A LYS 9 n 9 LYS 9 A PRO 10 n 10 PRO 10 A NH2 11 n 11 NH2 11 A author_defined_assembly 1 monomeric A THR 5 GLYCOSYLATION SITE A THR 5 THR A THR 7 GLYCOSYLATION SITE A THR 7 THR A THR 6 GLYCOSYLATION SITE A THR 6 THR A THR 4 GLYCOSYLATION SITE A THR 4 THR 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 2 A PRO 3 -44.57 165.65 3 A PRO 3 -44.52 91.55 3 A LYS 9 19.98 74.08 4 A PRO 3 -44.49 163.29 5 A PRO 3 -44.56 105.17 5 A LYS 8 42.91 96.21 7 A PRO 3 -44.63 150.99 7 A LYS 9 -175.82 46.65 8 A PRO 3 -42.29 151.21 9 A PRO 3 -42.59 156.73 10 A PRO 3 -43.98 155.02 10 A LYS 9 -175.86 46.55 11 A PRO 3 -44.59 95.82 11 A LYS 8 46.42 -146.92 11 A LYS 9 21.39 61.31 12 A PRO 3 -44.61 91.53 12 A LYS 8 47.36 -176.98 12 A LYS 9 -176.72 46.44 13 A PRO 3 -46.37 98.87 14 A PRO 3 -44.26 155.71 14 A LYS 8 73.08 166.21 15 A LYS 9 19.94 74.12 16 A LYS 9 21.36 61.22 closest to the average, model1 Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain 1 N N 2 N N 2 N N 2 N N 2 N N covale 1.305 both A ACE 1 A C ACE 1 1_555 A PRO 2 A N PRO 2 1_555 covale 1.410 one O-Glycosylation A THR 4 A OG1 THR 4 1_555 A A2G 101 B C1 A2G 1_555 covale 1.410 one O-Glycosylation A THR 5 A OG1 THR 5 1_555 A A2G 102 C C1 A2G 1_555 covale 1.410 one O-Glycosylation A THR 6 A OG1 THR 6 1_555 A A2G 103 D C1 A2G 1_555 covale 1.410 one O-Glycosylation A THR 7 A OG1 THR 7 1_555 A A2G 104 E C1 A2G 1_555 covale 1.306 both A PRO 10 A C PRO 10 1_555 A NH2 11 A N NH2 11 1_555 STRUCTURAL PROTEIN mucin domain, glycoprotein, glycosylation, alpha-dystroglycan, Tn antigen, N-acetyl-galactosamine, STRUCTURAL PROTEIN DAG1_HUMAN UNP 1 419 Q14118 PPTTTTKKP 419 427 2MK7 2 10 Q14118 A 1 2 10 1 acetylation ACE 1 2MK7 A Q14118 UNP 1 1 amidation NH2 11 2MK7 A Q14118 UNP 11