data_7DPP # _model_server_result.job_id t8hLRYGwBOLlmaiXCFqGFA _model_server_result.datetime_utc '2024-11-19 18:30:47' _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 7dpp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7DPP # _exptl.entry_id 7DPP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.235 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _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 115.25 _cell.angle_gamma 90 _cell.entry_id 7DPP _cell.length_a 97.16 _cell.length_b 83.253 _cell.length_c 51.688 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DPP _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 2_557 -x,y,-z+2 -1 0 0 0 1 0 0 0 -1 -44.09697 0 93.498955 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C19 _struct_conn.ptnr2_label_comp_id MYC _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MYC _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.769 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H10 O8' _chem_comp.formula_weight 318.235 _chem_comp.id MYC _chem_comp.mon_nstd_flag . _chem_comp.name 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE;3,3',4',5,5',7-HEXAHYDROXYFLAVONE;MYRICETIN;CANNABISCETIN" # 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 MYC doub 237 n y C1 C6 MYC sing 238 n y C1 H1 MYC sing 239 n n C2 C3 MYC sing 240 n y C2 O30 MYC sing 241 n n C3 C4 MYC doub 242 n y C3 C9 MYC sing 243 n y C4 C5 MYC sing 244 n y C4 O12 MYC sing 245 n y C5 C6 MYC doub 246 n y C5 H5 MYC sing 247 n n C6 O29 MYC sing 248 n n C9 C10 MYC sing 249 n y C9 O13 MYC doub 250 n n C10 C11 MYC doub 251 n y C10 O27 MYC sing 252 n n C11 C14 MYC sing 253 n y C11 O12 MYC sing 254 n y C14 C15 MYC doub 255 n y C14 C19 MYC sing 256 n y C15 C16 MYC sing 257 n y C15 H15 MYC sing 258 n n C16 C17 MYC doub 259 n y C16 O25 MYC sing 260 n n C17 C18 MYC sing 261 n y C17 O24 MYC sing 262 n n C18 C19 MYC doub 263 n y C18 O23 MYC sing 264 n n C19 H19 MYC sing 265 n n O23 HO3 MYC sing 266 n n O24 HO4 MYC sing 267 n n O25 HO5 MYC sing 268 n n O27 HO7 MYC sing 269 n n O29 HO9 MYC sing 270 n n O30 HO0 MYC sing 271 n n # _atom_sites.entry_id 7DPP _atom_sites.fract_transf_matrix[1][1] 0.010292 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012012 _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] 0.021391 _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 MYC A 1 401 401 MYC LIG . C 3 HOH A 1 501 20 HOH HOH . C 3 HOH A 2 502 45 HOH HOH . C 3 HOH A 3 503 27 HOH HOH . C 3 HOH A 4 504 18 HOH HOH . C 3 HOH A 5 505 37 HOH HOH . C 3 HOH A 6 506 33 HOH HOH . C 3 HOH A 7 507 14 HOH HOH . C 3 HOH A 8 508 32 HOH HOH . C 3 HOH A 9 509 47 HOH HOH . C 3 HOH A 10 510 63 HOH HOH . C 3 HOH A 11 511 10 HOH HOH . C 3 HOH A 12 512 5 HOH HOH . C 3 HOH A 13 513 21 HOH HOH . C 3 HOH A 14 514 3 HOH HOH . C 3 HOH A 15 515 31 HOH HOH . C 3 HOH A 16 516 53 HOH HOH . C 3 HOH A 17 517 2 HOH HOH . C 3 HOH A 18 518 16 HOH HOH . C 3 HOH A 19 519 4 HOH HOH . C 3 HOH A 20 520 48 HOH HOH . C 3 HOH A 21 521 39 HOH HOH . C 3 HOH A 22 522 30 HOH HOH . C 3 HOH A 23 523 50 HOH HOH . C 3 HOH A 24 524 17 HOH HOH . C 3 HOH A 25 525 41 HOH HOH . C 3 HOH A 26 526 25 HOH HOH . C 3 HOH A 27 527 34 HOH HOH . C 3 HOH A 28 528 1 HOH HOH . C 3 HOH A 29 529 6 HOH HOH . C 3 HOH A 30 530 23 HOH HOH . C 3 HOH A 31 531 19 HOH HOH . C 3 HOH A 32 532 9 HOH HOH . C 3 HOH A 33 533 8 HOH HOH . C 3 HOH A 34 534 52 HOH HOH . C 3 HOH A 35 535 26 HOH HOH . C 3 HOH A 36 536 65 HOH HOH . C 3 HOH A 37 537 13 HOH HOH . C 3 HOH A 38 538 62 HOH HOH . C 3 HOH A 39 539 42 HOH HOH . C 3 HOH A 40 540 56 HOH HOH . C 3 HOH A 41 541 38 HOH HOH . C 3 HOH A 42 542 28 HOH HOH . C 3 HOH A 43 543 35 HOH HOH . C 3 HOH A 44 544 7 HOH HOH . C 3 HOH A 45 545 15 HOH HOH . C 3 HOH A 46 546 66 HOH HOH . C 3 HOH A 47 547 55 HOH HOH . C 3 HOH A 48 548 40 HOH HOH . C 3 HOH A 49 549 12 HOH HOH . C 3 HOH A 50 550 11 HOH HOH . C 3 HOH A 51 551 44 HOH HOH . C 3 HOH A 52 552 29 HOH HOH . C 3 HOH A 53 553 59 HOH HOH . C 3 HOH A 54 554 24 HOH HOH . C 3 HOH A 55 555 49 HOH HOH . C 3 HOH A 56 556 58 HOH HOH . C 3 HOH A 57 557 67 HOH HOH . C 3 HOH A 58 558 36 HOH HOH . C 3 HOH A 59 559 46 HOH HOH . C 3 HOH A 60 560 22 HOH HOH . C 3 HOH A 61 561 51 HOH HOH . C 3 HOH A 62 562 57 HOH HOH . C 3 HOH A 63 563 64 HOH HOH . C 3 HOH A 64 564 43 HOH HOH . C 3 HOH A 65 565 60 HOH HOH . C 3 HOH A 66 566 54 HOH HOH . C 3 HOH A 67 567 61 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 MYC . . . B 2 -14.265 14.096 72.313 1 61.71 ? C1 MYC 401 A 1 HETATM 2 C C2 MYC . . . B 2 -14.895 15.133 71.667 1 60.93 ? C2 MYC 401 A 1 HETATM 3 C C3 MYC . . . B 2 -14.183 15.961 70.767 1 59.59 ? C3 MYC 401 A 1 HETATM 4 C C4 MYC . . . B 2 -12.832 15.677 70.565 1 61.16 ? C4 MYC 401 A 1 HETATM 5 C C5 MYC . . . B 2 -12.17 14.641 71.197 1 63.95 ? C5 MYC 401 A 1 HETATM 6 C C6 MYC . . . B 2 -12.904 13.854 72.074 1 64.24 ? C6 MYC 401 A 1 HETATM 7 C C9 MYC . . . B 2 -14.791 17.078 70.055 1 58.83 ? C9 MYC 401 A 1 HETATM 8 C C10 MYC . . . B 2 -13.929 17.817 69.174 1 57.99 ? C10 MYC 401 A 1 HETATM 9 C C11 MYC . . . B 2 -12.615 17.479 69.011 1 62.7 ? C11 MYC 401 A 1 HETATM 10 C C14 MYC . . . B 2 -11.662 18.184 68.142 1 62.18 ? C14 MYC 401 A 1 HETATM 11 C C15 MYC . . . B 2 -10.423 18.595 68.65 1 63.93 ? C15 MYC 401 A 1 HETATM 12 C C16 MYC . . . B 2 -9.523 19.264 67.845 1 65.08 ? C16 MYC 401 A 1 HETATM 13 C C17 MYC . . . B 2 -9.846 19.539 66.518 1 63.04 ? C17 MYC 401 A 1 HETATM 14 C C18 MYC . . . B 2 -11.078 19.134 66.005 1 62.94 ? C18 MYC 401 A 1 HETATM 15 C C19 MYC . . . B 2 -11.985 18.467 66.807 1 60.62 ? C19 MYC 401 A 1 HETATM 16 O O12 MYC . . . B 2 -12.077 16.433 69.716 1 63.13 ? O12 MYC 401 A 1 HETATM 17 O O13 MYC . . . B 2 -16.001 17.399 70.182 1 55.98 ? O13 MYC 401 A 1 HETATM 18 O O23 MYC . . . B 2 -11.348 19.424 64.696 1 63.75 ? O23 MYC 401 A 1 HETATM 19 O O24 MYC . . . B 2 -8.954 20.2 65.725 1 64.23 ? O24 MYC 401 A 1 HETATM 20 O O25 MYC . . . B 2 -8.304 19.676 68.311 1 66.78 ? O25 MYC 401 A 1 HETATM 21 O O27 MYC . . . B 2 -14.478 18.86 68.504 1 55.44 ? O27 MYC 401 A 1 HETATM 22 O O29 MYC . . . B 2 -12.297 12.83 72.717 1 65.91 ? O29 MYC 401 A 1 HETATM 23 O O30 MYC . . . B 2 -16.206 15.365 71.897 1 62.36 ? O30 MYC 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #