data_1KBG # _model_server_result.job_id uZyjc4wCIlMRJIwaABz2Bg _model_server_result.datetime_utc '2025-03-01 10:41:16' _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 1kbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 1KBG # _exptl.entry_id 1KBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 1KBG _cell.length_a 135.87 _cell.length_b 86.84 _cell.length_c 44.98 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 5 2 1 GLA GAL C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 A 1 NAG ? 100 NAG 4 n D NAG 2 A 2 NAG ? 101 NAG 4 n D FUC 3 A 3 FUC ? 102 FUC 5 n E GAL 1 B 1 GAL P 6 HGG 5 n E GLA 2 B 2 GLA P 6 HGG # 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 disulf ? disulf1 A SG CYS 101 H CYS 101 1_555 A SG CYS 164 H CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 203 H CYS 203 1_555 A SG CYS 259 H CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 25 L CYS 25 1_555 B SG CYS 80 L CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 86 H ASN 86 1_555 F C1 NAG . H NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 176 H ASN 176 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 C C TYR 5 P TYR 5 1_555 C N ESC 6 P ESC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 C C ESC 6 P ESC 6 1_555 C N GLY 7 P GLY 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 C CE ESC 6 P ESC 6 1_555 E O1 GAL . B GAL 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale6 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale7 D O6 NAG . A NAG 1 1_555 D C1 FUC . A FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale8 E O4 GAL . B GAL 1 1_555 E C1 GLA . B GLA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 sing # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 330 n n C1 O1 NAG sing 331 n n C1 O5 NAG sing 332 n n C1 H1 NAG sing 333 n n C2 C3 NAG sing 334 n n C2 N2 NAG sing 335 n n C2 H2 NAG sing 336 n n C3 C4 NAG sing 337 n n C3 O3 NAG sing 338 n n C3 H3 NAG sing 339 n n C4 C5 NAG sing 340 n n C4 O4 NAG sing 341 n n C4 H4 NAG sing 342 n n C5 C6 NAG sing 343 n n C5 O5 NAG sing 344 n n C5 H5 NAG sing 345 n n C6 O6 NAG sing 346 n n C6 H61 NAG sing 347 n n C6 H62 NAG sing 348 n n C7 C8 NAG sing 349 n n C7 N2 NAG sing 350 n n C7 O7 NAG doub 351 n n C8 H81 NAG sing 352 n n C8 H82 NAG sing 353 n n C8 H83 NAG sing 354 n n N2 HN2 NAG sing 355 n n O1 HO1 NAG sing 356 n n O3 HO3 NAG sing 357 n n O4 HO4 NAG sing 358 n n O6 HO6 NAG sing 359 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1KBG _atom_sites.fract_transf_matrix[1][1] 0.00736 _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] 0.011515 _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] 0.022232 _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 F 6 NAG H 1 1001 1 NAG NAG . G 7 HOH H 1 1103 1 HOH HOH . G 7 HOH H 2 1104 2 HOH HOH . G 7 HOH H 3 1105 4 HOH HOH . G 7 HOH H 4 1106 5 HOH HOH . G 7 HOH H 5 1107 7 HOH HOH . G 7 HOH H 6 1108 9 HOH HOH . G 7 HOH H 7 1109 10 HOH HOH . G 7 HOH H 8 1110 11 HOH HOH . G 7 HOH H 9 1111 12 HOH HOH . G 7 HOH H 10 1112 13 HOH HOH . G 7 HOH H 11 1113 14 HOH HOH . G 7 HOH H 12 1114 15 HOH HOH . G 7 HOH H 13 1115 16 HOH HOH . G 7 HOH H 14 1116 17 HOH HOH . G 7 HOH H 15 1117 18 HOH HOH . G 7 HOH H 16 1118 20 HOH HOH . G 7 HOH H 17 1119 21 HOH HOH . G 7 HOH H 18 1120 22 HOH HOH . G 7 HOH H 19 1121 23 HOH HOH . G 7 HOH H 20 1122 24 HOH HOH . G 7 HOH H 21 1123 25 HOH HOH . G 7 HOH H 22 1124 27 HOH HOH . G 7 HOH H 23 1125 28 HOH HOH . G 7 HOH H 24 1126 29 HOH HOH . G 7 HOH H 25 1127 30 HOH HOH . G 7 HOH H 26 1128 31 HOH HOH . G 7 HOH H 27 1129 33 HOH HOH . G 7 HOH H 28 1130 34 HOH HOH . G 7 HOH H 29 1131 35 HOH HOH . G 7 HOH H 30 1132 38 HOH HOH . G 7 HOH H 31 1133 39 HOH HOH . G 7 HOH H 32 1134 41 HOH HOH . G 7 HOH H 33 1135 42 HOH HOH . G 7 HOH H 34 1136 43 HOH HOH . G 7 HOH H 35 1137 44 HOH HOH . G 7 HOH H 36 1138 45 HOH HOH . G 7 HOH H 37 1139 47 HOH HOH . G 7 HOH H 38 1140 48 HOH HOH . G 7 HOH H 39 1141 50 HOH HOH . G 7 HOH H 40 1142 51 HOH HOH . G 7 HOH H 41 1143 53 HOH HOH . G 7 HOH H 42 1144 54 HOH HOH . G 7 HOH H 43 1145 55 HOH HOH . G 7 HOH H 44 1146 57 HOH HOH . G 7 HOH H 45 1147 59 HOH HOH . G 7 HOH H 46 1148 65 HOH HOH . G 7 HOH H 47 1149 66 HOH HOH . G 7 HOH H 48 1150 67 HOH HOH . G 7 HOH H 49 1151 68 HOH HOH . G 7 HOH H 50 1152 69 HOH HOH . G 7 HOH H 51 1153 70 HOH HOH . G 7 HOH H 52 1154 71 HOH HOH . G 7 HOH H 53 1155 72 HOH HOH . G 7 HOH H 54 1156 73 HOH HOH . G 7 HOH H 55 1157 74 HOH HOH . G 7 HOH H 56 1158 75 HOH HOH . G 7 HOH H 57 1159 76 HOH HOH . G 7 HOH H 58 1160 77 HOH HOH . G 7 HOH H 59 1161 78 HOH HOH . G 7 HOH H 60 1162 79 HOH HOH . G 7 HOH H 61 1163 80 HOH HOH . G 7 HOH H 62 1164 82 HOH HOH . G 7 HOH H 63 1165 83 HOH HOH . G 7 HOH H 64 1166 85 HOH HOH . G 7 HOH H 65 1167 86 HOH HOH . G 7 HOH H 66 1168 88 HOH HOH . G 7 HOH H 67 1169 89 HOH HOH . G 7 HOH H 68 1170 90 HOH HOH . G 7 HOH H 69 1171 91 HOH HOH . G 7 HOH H 70 1172 92 HOH HOH . G 7 HOH H 71 1173 93 HOH HOH . G 7 HOH H 72 1174 94 HOH HOH . G 7 HOH H 73 1175 96 HOH HOH . G 7 HOH H 74 1176 97 HOH HOH . G 7 HOH H 75 1177 100 HOH HOH . G 7 HOH H 76 1178 101 HOH HOH . G 7 HOH H 77 1179 103 HOH HOH . G 7 HOH H 78 1180 104 HOH HOH . G 7 HOH H 79 1181 105 HOH HOH . G 7 HOH H 80 1182 106 HOH HOH . G 7 HOH H 81 1183 108 HOH HOH . H 7 HOH L 1 100 3 HOH HOH . H 7 HOH L 2 101 6 HOH HOH . H 7 HOH L 3 102 8 HOH HOH . H 7 HOH L 4 103 19 HOH HOH . H 7 HOH L 5 104 26 HOH HOH . H 7 HOH L 6 105 32 HOH HOH . H 7 HOH L 7 106 36 HOH HOH . H 7 HOH L 8 107 37 HOH HOH . H 7 HOH L 9 108 40 HOH HOH . H 7 HOH L 10 109 46 HOH HOH . H 7 HOH L 11 110 49 HOH HOH . H 7 HOH L 12 111 52 HOH HOH . H 7 HOH L 13 112 56 HOH HOH . H 7 HOH L 14 113 58 HOH HOH . H 7 HOH L 15 114 60 HOH HOH . H 7 HOH L 16 115 61 HOH HOH . H 7 HOH L 17 116 62 HOH HOH . H 7 HOH L 18 117 63 HOH HOH . H 7 HOH L 19 118 64 HOH HOH . H 7 HOH L 20 119 81 HOH HOH . H 7 HOH L 21 120 84 HOH HOH . H 7 HOH L 22 121 98 HOH HOH . H 7 HOH L 23 122 102 HOH HOH . H 7 HOH L 24 123 107 HOH HOH . I 7 HOH P 1 87 87 HOH HOH . I 7 HOH P 2 95 95 HOH HOH . I 7 HOH P 3 99 99 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 NAG . . . F 6 25.437 47.189 -26.909 1 58.86 ? C1 NAG 1001 H 1 HETATM 2 C C2 NAG . . . F 6 25.787 47.121 -28.391 1 60.93 ? C2 NAG 1001 H 1 HETATM 3 C C3 NAG . . . F 6 24.505 47.235 -29.228 1 60.35 ? C3 NAG 1001 H 1 HETATM 4 C C4 NAG . . . F 6 23.462 46.21 -28.764 1 61.15 ? C4 NAG 1001 H 1 HETATM 5 C C5 NAG . . . F 6 23.282 46.23 -27.234 1 62.12 ? C5 NAG 1001 H 1 HETATM 6 C C6 NAG . . . F 6 22.422 45.066 -26.749 1 62.58 ? C6 NAG 1001 H 1 HETATM 7 C C7 NAG . . . F 6 26.481 49.45 -28.535 1 66.41 ? C7 NAG 1001 H 1 HETATM 8 C C8 NAG . . . F 6 27.571 50.417 -28.976 1 63.94 ? C8 NAG 1001 H 1 HETATM 9 N N2 NAG . . . F 6 26.741 48.16 -28.756 1 63.2 ? N2 NAG 1001 H 1 HETATM 10 O O3 NAG . . . F 6 24.816 46.987 -30.593 1 60.96 ? O3 NAG 1001 H 1 HETATM 11 O O4 NAG . . . F 6 22.213 46.463 -29.41 1 59.56 ? O4 NAG 1001 H 1 HETATM 12 O O5 NAG . . . F 6 24.565 46.105 -26.582 1 60.35 ? O5 NAG 1001 H 1 HETATM 13 O O6 NAG . . . F 6 22.226 45.092 -25.338 1 61.82 ? O6 NAG 1001 H 1 HETATM 14 O O7 NAG . . . F 6 25.451 49.858 -27.983 1 66.22 ? O7 NAG 1001 H 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #