data_6MGF # _model_server_result.job_id aDk5VhkJC-0hTPC9qkJ_VA _model_server_result.datetime_utc '2025-01-26 00:25:18' _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 6mgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 6MGF # _exptl.entry_id 6MGF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 586.63 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide' _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 100.07 _cell.angle_gamma 90 _cell.entry_id 6MGF _cell.length_a 102.742 _cell.length_b 34.767 _cell.length_c 62.897 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MGF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 metalc ? metalc1 A OG1 THR 43 A THR 43 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O3B ADP . A ADP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? # _chem_comp.formula 'C30 H38 N2 O10' _chem_comp.formula_weight 586.63 _chem_comp.id CZJ _chem_comp.mon_nstd_flag . _chem_comp.name '(3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'novobiocin derivative' # 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 C34 C32 CZJ sing 127 n n C34 C25 CZJ sing 128 n n C32 C33 CZJ sing 129 n n C32 C31 CZJ sing 130 n n C33 C29 CZJ sing 131 n n O21 C20 CZJ sing 132 n n O35 C24 CZJ doub 133 n n C18 C17 CZJ doub 134 n y C18 C19 CZJ sing 135 n y O13 C12 CZJ sing 136 n n C17 C16 CZJ sing 137 n y C31 C27 CZJ sing 138 n n C25 C24 CZJ sing 139 n n C25 C30 CZJ sing 140 n n C25 C26 CZJ sing 141 n n C24 N23 CZJ sing 142 n n O42 C14 CZJ sing 143 n n O42 C02 CZJ sing 144 n n C30 C29 CZJ sing 145 n n C29 C28 CZJ sing 146 n n C20 C19 CZJ sing 147 n n C20 C22 CZJ doub 148 n n C14 C12 CZJ sing 149 n n C14 O15 CZJ sing 150 n n C19 C39 CZJ doub 151 n y C12 C07 CZJ sing 152 n n C16 O15 CZJ sing 153 n n C16 C40 CZJ doub 154 n y C03 C02 CZJ sing 155 n n N23 C22 CZJ sing 156 n n C22 C36 CZJ sing 157 n n C26 C27 CZJ sing 158 n n C02 C04 CZJ sing 159 n n C02 C01 CZJ sing 160 n n C27 C28 CZJ sing 161 n n C39 C40 CZJ sing 162 n y C39 O37 CZJ sing 163 n n C40 C41 CZJ sing 164 n n C04 C07 CZJ sing 165 n n C04 O05 CZJ sing 166 n n C07 O08 CZJ sing 167 n n C36 O37 CZJ sing 168 n n C36 O38 CZJ doub 169 n n O08 C09 CZJ sing 170 n n O05 C06 CZJ sing 171 n n C09 O11 CZJ doub 172 n n C09 N10 CZJ sing 173 n n C17 H171 CZJ sing 174 n n C26 H262 CZJ sing 175 n n C26 H261 CZJ sing 176 n n C28 H282 CZJ sing 177 n n C28 H281 CZJ sing 178 n n C01 H013 CZJ sing 179 n n C01 H012 CZJ sing 180 n n C01 H011 CZJ sing 181 n n C03 H033 CZJ sing 182 n n C03 H031 CZJ sing 183 n n C03 H032 CZJ sing 184 n n C04 H041 CZJ sing 185 n n C06 H062 CZJ sing 186 n n C06 H063 CZJ sing 187 n n C06 H061 CZJ sing 188 n n C07 H071 CZJ sing 189 n n C12 H121 CZJ sing 190 n n C14 H141 CZJ sing 191 n n C18 H181 CZJ sing 192 n n C27 H271 CZJ sing 193 n n C29 H291 CZJ sing 194 n n C30 H302 CZJ sing 195 n n C30 H301 CZJ sing 196 n n C31 H311 CZJ sing 197 n n C31 H312 CZJ sing 198 n n C32 H321 CZJ sing 199 n n C33 H331 CZJ sing 200 n n C33 H332 CZJ sing 201 n n C34 H341 CZJ sing 202 n n C34 H342 CZJ sing 203 n n C41 H413 CZJ sing 204 n n C41 H411 CZJ sing 205 n n C41 H412 CZJ sing 206 n n N10 H101 CZJ sing 207 n n N10 H102 CZJ sing 208 n n N23 H231 CZJ sing 209 n n O13 H131 CZJ sing 210 n n O21 H211 CZJ sing 211 n n # _atom_sites.entry_id 6MGF _atom_sites.fract_transf_matrix[1][1] 0.009733 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001729 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028763 _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] 0.016148 _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 MG A 1 301 1 MG MG . C 3 ADP A 1 302 2 ADP ADP . D 4 CZJ A 1 303 3 CZJ CZJ . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 8 HOH HOH . E 5 HOH A 3 403 2 HOH HOH . E 5 HOH A 4 404 10 HOH HOH . E 5 HOH A 5 405 6 HOH HOH . E 5 HOH A 6 406 9 HOH HOH . E 5 HOH A 7 407 5 HOH HOH . E 5 HOH A 8 408 7 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 C17 CZJ . . . D 4 -2.908 -15.549 34.229 1 77.64 ? C17 CZJ 303 A 1 HETATM 2 C C20 CZJ . . . D 4 -2.367 -11.994 35.134 1 78.9 ? C20 CZJ 303 A 1 HETATM 3 C C22 CZJ . . . D 4 -1.624 -11.228 36.05 1 80.08 ? C22 CZJ 303 A 1 HETATM 4 C C24 CZJ . . . D 4 -2.542 -8.942 35.395 1 81.88 ? C24 CZJ 303 A 1 HETATM 5 C C26 CZJ . . . D 4 -3.569 -6.671 35.669 1 81.1 ? C26 CZJ 303 A 1 HETATM 6 C C28 CZJ . . . D 4 -3.568 -5.036 33.736 1 80.66 ? C28 CZJ 303 A 1 HETATM 7 C C01 CZJ . . . D 4 -5.448 -19.708 33.339 1 81.41 ? C01 CZJ 303 A 1 HETATM 8 C C02 CZJ . . . D 4 -4.282 -19.314 34.23 1 81.66 ? C02 CZJ 303 A 1 HETATM 9 C C03 CZJ . . . D 4 -4.861 -18.704 35.499 1 81.17 ? C03 CZJ 303 A 1 HETATM 10 C C04 CZJ . . . D 4 -3.489 -20.585 34.602 1 82.3 ? C04 CZJ 303 A 1 HETATM 11 C C06 CZJ . . . D 4 -4.4 -22.625 35.381 1 80.8 ? C06 CZJ 303 A 1 HETATM 12 C C07 CZJ . . . D 4 -2.102 -20.272 35.061 1 83.64 ? C07 CZJ 303 A 1 HETATM 13 C C09 CZJ . . . D 4 -0.778 -22.255 34.437 1 85.67 ? C09 CZJ 303 A 1 HETATM 14 C C12 CZJ . . . D 4 -1.41 -19.489 34.017 1 83.28 ? C12 CZJ 303 A 1 HETATM 15 C C14 CZJ . . . D 4 -2.074 -18.127 33.952 1 81.99 ? C14 CZJ 303 A 1 HETATM 16 C C16 CZJ . . . D 4 -2.11 -16.191 35.181 1 78.59 ? C16 CZJ 303 A 1 HETATM 17 C C18 CZJ . . . D 4 -2.995 -14.16 34.21 1 77.61 ? C18 CZJ 303 A 1 HETATM 18 C C19 CZJ . . . D 4 -2.26 -13.409 35.176 1 78.03 ? C19 CZJ 303 A 1 HETATM 19 C C25 CZJ . . . D 4 -2.361 -7.441 35.078 1 81.32 ? C25 CZJ 303 A 1 HETATM 20 C C27 CZJ . . . D 4 -3.617 -5.184 35.235 1 80.77 ? C27 CZJ 303 A 1 HETATM 21 C C29 CZJ . . . D 4 -2.378 -5.739 33.131 1 81.15 ? C29 CZJ 303 A 1 HETATM 22 C C30 CZJ . . . D 4 -2.258 -7.247 33.543 1 81.22 ? C30 CZJ 303 A 1 HETATM 23 C C31 CZJ . . . D 4 -2.282 -4.851 35.977 1 80.93 ? C31 CZJ 303 A 1 HETATM 24 C C32 CZJ . . . D 4 -1.035 -5.579 35.329 1 81.22 ? C32 CZJ 303 A 1 HETATM 25 C C33 CZJ . . . D 4 -1.003 -5.395 33.804 1 81.44 ? C33 CZJ 303 A 1 HETATM 26 C C34 CZJ . . . D 4 -1.138 -6.929 35.687 1 81.19 ? C34 CZJ 303 A 1 HETATM 27 C C36 CZJ . . . D 4 -0.755 -11.895 36.937 1 79.72 ? C36 CZJ 303 A 1 HETATM 28 C C39 CZJ . . . D 4 -1.487 -14.016 36.104 1 78.13 ? C39 CZJ 303 A 1 HETATM 29 C C40 CZJ . . . D 4 -1.396 -15.45 36.125 1 77.73 ? C40 CZJ 303 A 1 HETATM 30 C C41 CZJ . . . D 4 -0.531 -16.161 37.164 1 76.99 ? C41 CZJ 303 A 1 HETATM 31 N N10 CZJ . . . D 4 0.596 -22.01 34.03 1 85.95 ? N10 CZJ 303 A 1 HETATM 32 N N23 CZJ . . . D 4 -1.409 -9.796 35.764 1 81.24 ? N23 CZJ 303 A 1 HETATM 33 O O05 CZJ . . . D 4 -4.184 -21.266 35.641 1 81.55 ? O05 CZJ 303 A 1 HETATM 34 O O08 CZJ . . . D 4 -1.365 -21.48 35.447 1 84.91 ? O08 CZJ 303 A 1 HETATM 35 O O11 CZJ . . . D 4 -1.398 -23.123 33.918 1 85.68 ? O11 CZJ 303 A 1 HETATM 36 O O13 CZJ . . . D 4 -1.665 -20.101 32.749 1 84.01 ? O13 CZJ 303 A 1 HETATM 37 O O15 CZJ . . . D 4 -2.024 -17.596 35.207 1 80.48 ? O15 CZJ 303 A 1 HETATM 38 O O21 CZJ . . . D 4 -3.345 -11.437 34.298 1 78.41 ? O21 CZJ 303 A 1 HETATM 39 O O35 CZJ . . . D 4 -3.631 -9.4 35.327 1 82.32 ? O35 CZJ 303 A 1 HETATM 40 O O37 CZJ . . . D 4 -0.781 -13.26 37.034 1 78.82 ? O37 CZJ 303 A 1 HETATM 41 O O38 CZJ . . . D 4 0 -11.276 37.616 1 79.86 ? O38 CZJ 303 A 1 HETATM 42 O O42 CZJ . . . D 4 -3.493 -18.292 33.5 1 81.86 ? O42 CZJ 303 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #