data_2OFD # _model_server_result.job_id QQsX4B-cogVdbK0qG-9XvA _model_server_result.datetime_utc '2024-10-19 13:20:02' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2ofd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":144}' # _entry.id 2OFD # _exptl.entry_id 2OFD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-galactopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2OFD _cell.length_a 99.485 _cell.length_b 99.485 _cell.length_c 64.007 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OFD _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 64.007 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C ACE 1 A ACE 0 1_555 A N THR 2 A THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 B C ACE 1 B ACE 0 1_555 B N THR 2 B THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NGA _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-galactopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-galactosamine;2-acetamido-2-deoxy-beta-D-galactose;2-acetamido-2-deoxy-D-galactose;2-acetamido-2-deoxy-galactose;N-ACETYL-D-GALACTOSAMINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 NGA sing 249 n n C1 O1 NGA sing 250 n n C1 O5 NGA sing 251 n n C1 H1 NGA sing 252 n n C2 C3 NGA sing 253 n n C2 N2 NGA sing 254 n n C2 H2 NGA sing 255 n n C3 C4 NGA sing 256 n n C3 O3 NGA sing 257 n n C3 H3 NGA sing 258 n n C4 C5 NGA sing 259 n n C4 O4 NGA sing 260 n n C4 H4 NGA sing 261 n n C5 C6 NGA sing 262 n n C5 O5 NGA sing 263 n n C5 H5 NGA sing 264 n n C6 O6 NGA sing 265 n n C6 H61 NGA sing 266 n n C6 H62 NGA sing 267 n n C7 C8 NGA sing 268 n n C7 N2 NGA sing 269 n n C7 O7 NGA doub 270 n n C8 H81 NGA sing 271 n n C8 H82 NGA sing 272 n n C8 H83 NGA sing 273 n n N2 HN2 NGA sing 274 n n O1 HO1 NGA sing 275 n n O3 HO3 NGA sing 276 n n O4 HO4 NGA sing 277 n n O6 HO6 NGA sing 278 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NGA DGalpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NGA N-acetyl-b-D-galactopyranosamine 'COMMON NAME' GMML 1 NGA b-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NGA GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2OFD _atom_sites.fract_transf_matrix[1][1] 0.010052 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010052 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015623 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NGA A 1 144 144 NGA NGA . D 3 ACT A 1 997 997 ACT ACT . E 2 NGA B 1 144 144 NGA NGA . F 2 NGA B 1 145 145 NGA NGA . G 3 ACT B 1 995 995 ACT ACT . H 3 ACT B 1 996 996 ACT ACT . I 4 HOH A 1 998 2 HOH HOH . I 4 HOH A 2 999 4 HOH HOH . I 4 HOH A 3 1000 5 HOH HOH . I 4 HOH A 4 1001 7 HOH HOH . I 4 HOH A 5 1002 10 HOH HOH . I 4 HOH A 6 1003 11 HOH HOH . I 4 HOH A 7 1004 12 HOH HOH . I 4 HOH A 8 1005 13 HOH HOH . I 4 HOH A 9 1006 21 HOH HOH . I 4 HOH A 10 1007 23 HOH HOH . I 4 HOH A 11 1008 28 HOH HOH . I 4 HOH A 12 1009 30 HOH HOH . I 4 HOH A 13 1010 31 HOH HOH . I 4 HOH A 14 1011 32 HOH HOH . I 4 HOH A 15 1012 37 HOH HOH . I 4 HOH A 16 1013 38 HOH HOH . I 4 HOH A 17 1014 39 HOH HOH . I 4 HOH A 18 1015 45 HOH HOH . I 4 HOH A 19 1016 47 HOH HOH . I 4 HOH A 20 1017 48 HOH HOH . I 4 HOH A 21 1018 49 HOH HOH . I 4 HOH A 22 1019 51 HOH HOH . I 4 HOH A 23 1020 54 HOH HOH . I 4 HOH A 24 1021 55 HOH HOH . I 4 HOH A 25 1022 59 HOH HOH . I 4 HOH A 26 1023 60 HOH HOH . I 4 HOH A 27 1024 61 HOH HOH . I 4 HOH A 28 1025 62 HOH HOH . I 4 HOH A 29 1026 64 HOH HOH . I 4 HOH A 30 1027 65 HOH HOH . I 4 HOH A 31 1028 66 HOH HOH . I 4 HOH A 32 1029 67 HOH HOH . I 4 HOH A 33 1030 71 HOH HOH . I 4 HOH A 34 1031 77 HOH HOH . I 4 HOH A 35 1032 79 HOH HOH . I 4 HOH A 36 1033 86 HOH HOH . I 4 HOH A 37 1034 87 HOH HOH . I 4 HOH A 38 1035 89 HOH HOH . I 4 HOH A 39 1036 91 HOH HOH . I 4 HOH A 40 1037 92 HOH HOH . I 4 HOH A 41 1038 93 HOH HOH . I 4 HOH A 42 1039 97 HOH HOH . I 4 HOH A 43 1040 98 HOH HOH . I 4 HOH A 44 1041 103 HOH HOH . I 4 HOH A 45 1042 105 HOH HOH . I 4 HOH A 46 1043 106 HOH HOH . I 4 HOH A 47 1044 112 HOH HOH . I 4 HOH A 48 1045 114 HOH HOH . I 4 HOH A 49 1046 116 HOH HOH . I 4 HOH A 50 1047 118 HOH HOH . I 4 HOH A 51 1048 121 HOH HOH . I 4 HOH A 52 1049 122 HOH HOH . I 4 HOH A 53 1050 123 HOH HOH . I 4 HOH A 54 1051 124 HOH HOH . I 4 HOH A 55 1052 125 HOH HOH . I 4 HOH A 56 1053 130 HOH HOH . I 4 HOH A 57 1054 133 HOH HOH . I 4 HOH A 58 1055 135 HOH HOH . I 4 HOH A 59 1056 136 HOH HOH . I 4 HOH A 60 1057 137 HOH HOH . I 4 HOH A 61 1058 139 HOH HOH . I 4 HOH A 62 1059 140 HOH HOH . I 4 HOH A 63 1060 141 HOH HOH . I 4 HOH A 64 1061 145 HOH HOH . I 4 HOH A 65 1062 146 HOH HOH . I 4 HOH A 66 1063 147 HOH HOH . I 4 HOH A 67 1064 150 HOH HOH . I 4 HOH A 68 1065 155 HOH HOH . I 4 HOH A 69 1066 156 HOH HOH . I 4 HOH A 70 1067 157 HOH HOH . I 4 HOH A 71 1068 159 HOH HOH . I 4 HOH A 72 1069 160 HOH HOH . I 4 HOH A 73 1070 163 HOH HOH . I 4 HOH A 74 1071 164 HOH HOH . I 4 HOH A 75 1072 168 HOH HOH . I 4 HOH A 76 1073 170 HOH HOH . I 4 HOH A 77 1074 173 HOH HOH . I 4 HOH A 78 1075 174 HOH HOH . I 4 HOH A 79 1076 175 HOH HOH . I 4 HOH A 80 1077 178 HOH HOH . I 4 HOH A 81 1078 180 HOH HOH . I 4 HOH A 82 1079 183 HOH HOH . I 4 HOH A 83 1080 184 HOH HOH . I 4 HOH A 84 1081 185 HOH HOH . I 4 HOH A 85 1082 186 HOH HOH . I 4 HOH A 86 1083 188 HOH HOH . I 4 HOH A 87 1084 189 HOH HOH . I 4 HOH A 88 1085 194 HOH HOH . I 4 HOH A 89 1086 195 HOH HOH . J 4 HOH B 1 997 1 HOH HOH . J 4 HOH B 2 998 3 HOH HOH . J 4 HOH B 3 999 6 HOH HOH . J 4 HOH B 4 1000 8 HOH HOH . J 4 HOH B 5 1001 9 HOH HOH . J 4 HOH B 6 1002 14 HOH HOH . J 4 HOH B 7 1003 15 HOH HOH . J 4 HOH B 8 1004 16 HOH HOH . J 4 HOH B 9 1005 17 HOH HOH . J 4 HOH B 10 1006 18 HOH HOH . J 4 HOH B 11 1007 19 HOH HOH . J 4 HOH B 12 1008 20 HOH HOH . J 4 HOH B 13 1009 22 HOH HOH . J 4 HOH B 14 1010 24 HOH HOH . J 4 HOH B 15 1011 25 HOH HOH . J 4 HOH B 16 1012 27 HOH HOH . J 4 HOH B 17 1013 29 HOH HOH . J 4 HOH B 18 1014 33 HOH HOH . J 4 HOH B 19 1015 34 HOH HOH . J 4 HOH B 20 1016 35 HOH HOH . J 4 HOH B 21 1017 36 HOH HOH . J 4 HOH B 22 1018 40 HOH HOH . J 4 HOH B 23 1019 42 HOH HOH . J 4 HOH B 24 1020 43 HOH HOH . J 4 HOH B 25 1021 44 HOH HOH . J 4 HOH B 26 1022 46 HOH HOH . J 4 HOH B 27 1023 50 HOH HOH . J 4 HOH B 28 1024 52 HOH HOH . J 4 HOH B 29 1025 53 HOH HOH . J 4 HOH B 30 1026 56 HOH HOH . J 4 HOH B 31 1027 57 HOH HOH . J 4 HOH B 32 1028 58 HOH HOH . J 4 HOH B 33 1029 63 HOH HOH . J 4 HOH B 34 1030 69 HOH HOH . J 4 HOH B 35 1031 70 HOH HOH . J 4 HOH B 36 1032 72 HOH HOH . J 4 HOH B 37 1033 73 HOH HOH . J 4 HOH B 38 1034 75 HOH HOH . J 4 HOH B 39 1035 76 HOH HOH . J 4 HOH B 40 1036 78 HOH HOH . J 4 HOH B 41 1037 80 HOH HOH . J 4 HOH B 42 1038 81 HOH HOH . J 4 HOH B 43 1039 82 HOH HOH . J 4 HOH B 44 1040 83 HOH HOH . J 4 HOH B 45 1041 84 HOH HOH . J 4 HOH B 46 1042 85 HOH HOH . J 4 HOH B 47 1043 88 HOH HOH . J 4 HOH B 48 1044 90 HOH HOH . J 4 HOH B 49 1045 94 HOH HOH . J 4 HOH B 50 1046 95 HOH HOH . J 4 HOH B 51 1047 96 HOH HOH . J 4 HOH B 52 1048 99 HOH HOH . J 4 HOH B 53 1049 100 HOH HOH . J 4 HOH B 54 1050 101 HOH HOH . J 4 HOH B 55 1051 104 HOH HOH . J 4 HOH B 56 1052 107 HOH HOH . J 4 HOH B 57 1053 108 HOH HOH . J 4 HOH B 58 1054 109 HOH HOH . J 4 HOH B 59 1055 110 HOH HOH . J 4 HOH B 60 1056 111 HOH HOH . J 4 HOH B 61 1057 113 HOH HOH . J 4 HOH B 62 1058 115 HOH HOH . J 4 HOH B 63 1059 120 HOH HOH . J 4 HOH B 64 1060 126 HOH HOH . J 4 HOH B 65 1061 127 HOH HOH . J 4 HOH B 66 1062 128 HOH HOH . J 4 HOH B 67 1063 129 HOH HOH . J 4 HOH B 68 1064 131 HOH HOH . J 4 HOH B 69 1065 132 HOH HOH . J 4 HOH B 70 1066 134 HOH HOH . J 4 HOH B 71 1067 138 HOH HOH . J 4 HOH B 72 1068 142 HOH HOH . J 4 HOH B 73 1069 143 HOH HOH . J 4 HOH B 74 1070 144 HOH HOH . J 4 HOH B 75 1071 148 HOH HOH . J 4 HOH B 76 1072 149 HOH HOH . J 4 HOH B 77 1073 151 HOH HOH . J 4 HOH B 78 1074 152 HOH HOH . J 4 HOH B 79 1075 153 HOH HOH . J 4 HOH B 80 1076 154 HOH HOH . J 4 HOH B 81 1077 158 HOH HOH . J 4 HOH B 82 1078 161 HOH HOH . J 4 HOH B 83 1079 162 HOH HOH . J 4 HOH B 84 1080 165 HOH HOH . J 4 HOH B 85 1081 166 HOH HOH . J 4 HOH B 86 1082 167 HOH HOH . J 4 HOH B 87 1083 169 HOH HOH . J 4 HOH B 88 1084 171 HOH HOH . J 4 HOH B 89 1085 172 HOH HOH . J 4 HOH B 90 1086 177 HOH HOH . J 4 HOH B 91 1087 179 HOH HOH . J 4 HOH B 92 1088 181 HOH HOH . J 4 HOH B 93 1089 182 HOH HOH . J 4 HOH B 94 1090 187 HOH HOH . J 4 HOH B 95 1091 190 HOH HOH . J 4 HOH B 96 1092 191 HOH HOH . J 4 HOH B 97 1093 192 HOH HOH . J 4 HOH B 98 1094 193 HOH HOH . J 4 HOH B 99 1095 196 HOH HOH . J 4 HOH B 100 1096 197 HOH HOH . J 4 HOH B 101 1097 198 HOH HOH . J 4 HOH B 102 1098 199 HOH HOH . J 4 HOH B 103 1099 200 HOH HOH . J 4 HOH B 104 1100 201 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 NGA . . . C 2 27.418 -7.05 17.171 1 21.43 ? C1 NGA 144 A 1 HETATM 2 C C2 NGA . . . C 2 26.31 -6.004 17.033 1 20.93 ? C2 NGA 144 A 1 HETATM 3 C C3 NGA . . . C 2 26.538 -5.141 15.792 1 20.23 ? C3 NGA 144 A 1 HETATM 4 C C4 NGA . . . C 2 27.932 -4.524 15.811 1 21.14 ? C4 NGA 144 A 1 HETATM 5 C C5 NGA . . . C 2 29.012 -5.583 16.053 1 21.59 ? C5 NGA 144 A 1 HETATM 6 C C6 NGA . . . C 2 30.327 -4.897 16.365 1 23.48 ? C6 NGA 144 A 1 HETATM 7 C C7 NGA . . . C 2 24.195 -6.621 18.119 1 20.35 ? C7 NGA 144 A 1 HETATM 8 C C8 NGA . . . C 2 22.81 -7.16 17.917 1 19.85 ? C8 NGA 144 A 1 HETATM 9 N N2 NGA . . . C 2 24.983 -6.603 17.038 1 20.41 ? N2 NGA 144 A 1 HETATM 10 O O1 NGA . . . C 2 27.378 -7.991 16.089 1 22.22 ? O1 NGA 144 A 1 HETATM 11 O O3 NGA . . . C 2 25.564 -4.099 15.759 1 20.84 ? O3 NGA 144 A 1 HETATM 12 O O4 NGA . . . C 2 28.008 -3.511 16.836 1 19.74 ? O4 NGA 144 A 1 HETATM 13 O O5 NGA . . . C 2 28.697 -6.406 17.184 1 20.83 ? O5 NGA 144 A 1 HETATM 14 O O6 NGA . . . C 2 31.298 -5.252 15.393 1 26.96 ? O6 NGA 144 A 1 HETATM 15 O O7 NGA . . . C 2 24.559 -6.235 19.22 1 19.67 ? O7 NGA 144 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #