data_4HMD # _model_server_result.job_id SLyY2v1TPpRHyW4Ru8Koxg _model_server_result.datetime_utc '2024-11-07 02:47:40' _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 4hmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":902}' # _entry.id 4HMD # _exptl.entry_id 4HMD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 204.2 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE _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 120 _cell.entry_id 4HMD _cell.length_a 67.091 _cell.length_b 67.091 _cell.length_c 258.033 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 5_555 -x+y,y,-z+1/3 -1 0 0 0 1 0 0 0 -1 0 0 86.011 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 19 A CYS 41 1_555 A SG CYS 31 A CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? covale ? covale1 B C1 NAG . A NAG 901 1_555 C O4 NGO . A NGO 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? metalc ? metalc1 A O THR 2 A THR 24 1_555 D NA NA . A NA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc2 A OD1 ASN 83 A ASN 105 1_555 D NA NA . A NA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc3 A O GLY 122 A GLY 144 1_555 D NA NA . A NA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc4 A OD1 ASP 124 A ASP 146 1_555 D NA NA . A NA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc5 D NA NA . A NA 903 1_555 F O HOH . A HOH 1132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? # _chem_comp.formula 'C8 H14 N O5 1' _chem_comp.formula_weight 204.2 _chem_comp.id NGO _chem_comp.mon_nstd_flag . _chem_comp.name 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE' # 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 NGO sing 280 n n C1 O1 NGO sing 281 n n C1 O5 NGO sing 282 n n C1 HC1 NGO sing 283 n n C2 C3 NGO sing 284 n n C2 N2 NGO sing 285 n n C2 HC2 NGO sing 286 n n C3 C4 NGO sing 287 n n C3 O3 NGO sing 288 n n C3 HC3 NGO sing 289 n n C4 C5 NGO sing 290 n n C4 O4 NGO sing 291 n n C4 HC4 NGO sing 292 n n C5 C6 NGO sing 293 n n C5 O5 NGO sing 294 n n C5 HC5 NGO sing 295 n n C6 O6 NGO sing 296 n n C6 HC61 NGO sing 297 n n C6 HC62 NGO sing 298 n n C7 C8 NGO sing 299 n n C7 N2 NGO doub 300 n n C7 O1 NGO sing 301 n n C8 HC81 NGO sing 302 n n C8 HC82 NGO sing 303 n n C8 HC83 NGO sing 304 n n N2 HN NGO sing 305 n n O3 HO3 NGO sing 306 n n O4 HO4 NGO sing 307 n n O6 HO6 NGO sing 308 n n # _atom_sites.entry_id 4HMD _atom_sites.fract_transf_matrix[1][1] 0.014905 _atom_sites.fract_transf_matrix[1][2] 0.008605 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017211 _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] 0.003875 _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 B 2 NAG A 1 901 901 NAG NAG . C 3 NGO A 1 902 902 NGO NGO . D 4 NA A 1 903 903 NA NA . E 5 GOL A 1 904 904 GOL GOL . F 6 HOH A 1 1001 1001 HOH HOH . F 6 HOH A 2 1002 1002 HOH HOH . F 6 HOH A 3 1003 1003 HOH HOH . F 6 HOH A 4 1004 1004 HOH HOH . F 6 HOH A 5 1005 1005 HOH HOH . F 6 HOH A 6 1006 1006 HOH HOH . F 6 HOH A 7 1007 1007 HOH HOH . F 6 HOH A 8 1008 1008 HOH HOH . F 6 HOH A 9 1009 1009 HOH HOH . F 6 HOH A 10 1010 1010 HOH HOH . F 6 HOH A 11 1011 1011 HOH HOH . F 6 HOH A 12 1012 1012 HOH HOH . F 6 HOH A 13 1013 1013 HOH HOH . F 6 HOH A 14 1014 1014 HOH HOH . F 6 HOH A 15 1015 1015 HOH HOH . F 6 HOH A 16 1016 1016 HOH HOH . F 6 HOH A 17 1017 1017 HOH HOH . F 6 HOH A 18 1018 1018 HOH HOH . F 6 HOH A 19 1019 1019 HOH HOH . F 6 HOH A 20 1020 1020 HOH HOH . F 6 HOH A 21 1021 1021 HOH HOH . F 6 HOH A 22 1022 1022 HOH HOH . F 6 HOH A 23 1023 1023 HOH HOH . F 6 HOH A 24 1024 1024 HOH HOH . F 6 HOH A 25 1025 1025 HOH HOH . F 6 HOH A 26 1026 1026 HOH HOH . F 6 HOH A 27 1027 1027 HOH HOH . F 6 HOH A 28 1028 1028 HOH HOH . F 6 HOH A 29 1029 1029 HOH HOH . F 6 HOH A 30 1030 1030 HOH HOH . F 6 HOH A 31 1031 1031 HOH HOH . F 6 HOH A 32 1032 1032 HOH HOH . F 6 HOH A 33 1033 1033 HOH HOH . F 6 HOH A 34 1034 1034 HOH HOH . F 6 HOH A 35 1035 1035 HOH HOH . F 6 HOH A 36 1036 1036 HOH HOH . F 6 HOH A 37 1037 1037 HOH HOH . F 6 HOH A 38 1038 1038 HOH HOH . F 6 HOH A 39 1039 1039 HOH HOH . F 6 HOH A 40 1040 1040 HOH HOH . F 6 HOH A 41 1041 1041 HOH HOH . F 6 HOH A 42 1042 1042 HOH HOH . F 6 HOH A 43 1043 1043 HOH HOH . F 6 HOH A 44 1044 1044 HOH HOH . F 6 HOH A 45 1045 1045 HOH HOH . F 6 HOH A 46 1046 1046 HOH HOH . F 6 HOH A 47 1047 1047 HOH HOH . F 6 HOH A 48 1048 1048 HOH HOH . F 6 HOH A 49 1049 1049 HOH HOH . F 6 HOH A 50 1050 1050 HOH HOH . F 6 HOH A 51 1051 1051 HOH HOH . F 6 HOH A 52 1052 1052 HOH HOH . F 6 HOH A 53 1053 1053 HOH HOH . F 6 HOH A 54 1054 1054 HOH HOH . F 6 HOH A 55 1055 1055 HOH HOH . F 6 HOH A 56 1056 1056 HOH HOH . F 6 HOH A 57 1057 1057 HOH HOH . F 6 HOH A 58 1058 1058 HOH HOH . F 6 HOH A 59 1059 1059 HOH HOH . F 6 HOH A 60 1060 1060 HOH HOH . F 6 HOH A 61 1061 1061 HOH HOH . F 6 HOH A 62 1062 1062 HOH HOH . F 6 HOH A 63 1063 1063 HOH HOH . F 6 HOH A 64 1064 1064 HOH HOH . F 6 HOH A 65 1065 1065 HOH HOH . F 6 HOH A 66 1066 1066 HOH HOH . F 6 HOH A 67 1067 1067 HOH HOH . F 6 HOH A 68 1068 1068 HOH HOH . F 6 HOH A 69 1069 1069 HOH HOH . F 6 HOH A 70 1070 1070 HOH HOH . F 6 HOH A 71 1071 1071 HOH HOH . F 6 HOH A 72 1072 1072 HOH HOH . F 6 HOH A 73 1073 1073 HOH HOH . F 6 HOH A 74 1074 1074 HOH HOH . F 6 HOH A 75 1075 1075 HOH HOH . F 6 HOH A 76 1076 1076 HOH HOH . F 6 HOH A 77 1077 1077 HOH HOH . F 6 HOH A 78 1078 1078 HOH HOH . F 6 HOH A 79 1079 1079 HOH HOH . F 6 HOH A 80 1080 1080 HOH HOH . F 6 HOH A 81 1081 1081 HOH HOH . F 6 HOH A 82 1082 1082 HOH HOH . F 6 HOH A 83 1083 1083 HOH HOH . F 6 HOH A 84 1084 1084 HOH HOH . F 6 HOH A 85 1085 1085 HOH HOH . F 6 HOH A 86 1086 1086 HOH HOH . F 6 HOH A 87 1087 1087 HOH HOH . F 6 HOH A 88 1088 1088 HOH HOH . F 6 HOH A 89 1089 1089 HOH HOH . F 6 HOH A 90 1090 1090 HOH HOH . F 6 HOH A 91 1091 1091 HOH HOH . F 6 HOH A 92 1092 1092 HOH HOH . F 6 HOH A 93 1093 1093 HOH HOH . F 6 HOH A 94 1094 1094 HOH HOH . F 6 HOH A 95 1095 1095 HOH HOH . F 6 HOH A 96 1096 1096 HOH HOH . F 6 HOH A 97 1097 1097 HOH HOH . F 6 HOH A 98 1098 1098 HOH HOH . F 6 HOH A 99 1099 1099 HOH HOH . F 6 HOH A 100 1100 1100 HOH HOH . F 6 HOH A 101 1101 1101 HOH HOH . F 6 HOH A 102 1102 1102 HOH HOH . F 6 HOH A 103 1103 1103 HOH HOH . F 6 HOH A 104 1104 1104 HOH HOH . F 6 HOH A 105 1105 1105 HOH HOH . F 6 HOH A 106 1106 1106 HOH HOH . F 6 HOH A 107 1107 1107 HOH HOH . F 6 HOH A 108 1108 1108 HOH HOH . F 6 HOH A 109 1109 1109 HOH HOH . F 6 HOH A 110 1110 1110 HOH HOH . F 6 HOH A 111 1111 1111 HOH HOH . F 6 HOH A 112 1112 1112 HOH HOH . F 6 HOH A 113 1113 1113 HOH HOH . F 6 HOH A 114 1114 1114 HOH HOH . F 6 HOH A 115 1115 1115 HOH HOH . F 6 HOH A 116 1116 1116 HOH HOH . F 6 HOH A 117 1117 1117 HOH HOH . F 6 HOH A 118 1118 1118 HOH HOH . F 6 HOH A 119 1119 1119 HOH HOH . F 6 HOH A 120 1120 1120 HOH HOH . F 6 HOH A 121 1121 1121 HOH HOH . F 6 HOH A 122 1122 1122 HOH HOH . F 6 HOH A 123 1123 1123 HOH HOH . F 6 HOH A 124 1124 1124 HOH HOH . F 6 HOH A 125 1125 1125 HOH HOH . F 6 HOH A 126 1126 1126 HOH HOH . F 6 HOH A 127 1127 1127 HOH HOH . F 6 HOH A 128 1128 1128 HOH HOH . F 6 HOH A 129 1129 1129 HOH HOH . F 6 HOH A 130 1130 1130 HOH HOH . F 6 HOH A 131 1131 1131 HOH HOH . F 6 HOH A 132 1132 1132 HOH HOH . F 6 HOH A 133 1133 1133 HOH HOH . F 6 HOH A 134 1134 1134 HOH HOH . F 6 HOH A 135 1135 1135 HOH HOH . F 6 HOH A 136 1136 1136 HOH HOH . F 6 HOH A 137 1137 1137 HOH HOH . F 6 HOH A 138 1138 1138 HOH HOH . F 6 HOH A 139 1139 1139 HOH HOH . F 6 HOH A 140 1140 1140 HOH HOH . F 6 HOH A 141 1141 1141 HOH HOH . F 6 HOH A 142 1142 1142 HOH HOH . F 6 HOH A 143 1143 1143 HOH HOH . F 6 HOH A 144 1144 1144 HOH HOH . F 6 HOH A 145 1145 1145 HOH HOH . F 6 HOH A 146 1146 1146 HOH HOH . F 6 HOH A 147 1147 1147 HOH HOH . F 6 HOH A 148 1148 1148 HOH HOH . F 6 HOH A 149 1149 1149 HOH HOH . F 6 HOH A 150 1150 1150 HOH HOH . F 6 HOH A 151 1151 1151 HOH HOH . F 6 HOH A 152 1152 1152 HOH HOH . F 6 HOH A 153 1153 1153 HOH HOH . F 6 HOH A 154 1154 1154 HOH HOH . F 6 HOH A 155 1155 1155 HOH HOH . F 6 HOH A 156 1156 1156 HOH HOH . F 6 HOH A 157 1157 1157 HOH HOH . F 6 HOH A 158 1158 1158 HOH HOH . F 6 HOH A 159 1159 1159 HOH HOH . F 6 HOH A 160 1160 1160 HOH HOH . F 6 HOH A 161 1161 1161 HOH HOH . F 6 HOH A 162 1162 1162 HOH HOH . F 6 HOH A 163 1163 1163 HOH HOH . F 6 HOH A 164 1164 1164 HOH HOH . F 6 HOH A 165 1165 1165 HOH HOH . F 6 HOH A 166 1166 1166 HOH HOH . F 6 HOH A 167 1167 1167 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 NGO . . . C 3 1.161 32.056 28.78 1 66.01 ? C1 NGO 902 A 1 HETATM 2 C C2 NGO . . . C 3 -0.135 32.57 28.107 1 60.71 ? C2 NGO 902 A 1 HETATM 3 C C3 NGO . . . C 3 -0.003 34.026 27.588 1 53.64 ? C3 NGO 902 A 1 HETATM 4 C C4 NGO . . . C 3 0.962 34.916 28.396 1 61.05 ? C4 NGO 902 A 1 HETATM 5 C C5 NGO . . . C 3 2.259 34.233 28.859 1 55.72 ? C5 NGO 902 A 1 HETATM 6 C C6 NGO . . . C 3 2.99 35.209 29.793 1 52.45 ? C6 NGO 902 A 1 HETATM 7 C C7 NGO . . . C 3 0.884 30.88 26.809 1 52.52 ? C7 NGO 902 A 1 HETATM 8 C C8 NGO . . . C 3 1.116 29.756 25.829 1 55.56 ? C8 NGO 902 A 1 HETATM 9 N N2 NGO . . . C 3 -0.295 31.536 27.032 1 53.92 ? N2 NGO 902 A 1 HETATM 10 O O1 NGO . . . C 3 1.931 31.365 27.712 1 57.5 ? O1 NGO 902 A 1 HETATM 11 O O3 NGO . . . C 3 -1.274 34.703 27.578 1 54.88 ? O3 NGO 902 A 1 HETATM 12 O O4 NGO . . . C 3 1.319 36.098 27.624 1 59.16 ? O4 NGO 902 A 1 HETATM 13 O O5 NGO . . . C 3 1.897 33.036 29.537 1 57.5 ? O5 NGO 902 A 1 HETATM 14 O O6 NGO . . . C 3 4.428 35.101 29.712 1 54.87 ? O6 NGO 902 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #