data_5CCW # _model_server_result.job_id WfkjM1nKAD4_zQDTMA6xEQ _model_server_result.datetime_utc '2024-12-26 18:05:26' _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 5ccw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":105}' # _entry.id 5CCW # _exptl.entry_id 5CCW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 613.401 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Au(caffein-2-ylidene)2 _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 5CCW _cell.length_a 47.129 _cell.length_b 51.286 _cell.length_c 58.768 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CCW _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 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 metalc ? metalc1 A O6 DG 3 A DG 3 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc2 A O6 DG 4 A DG 4 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc3 A O6 DG 4 A DG 4 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc4 A O6 DG 5 A DG 5 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc5 A O6 DG 9 A DG 9 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc6 A O6 DG 10 A DG 10 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc7 A O6 DG 10 A DG 10 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.001 ? metalc ? metalc8 A O6 DG 11 A DG 11 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc9 A O6 DG 15 A DG 15 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc10 A O6 DG 16 A DG 16 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc11 A O6 DG 16 A DG 16 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc12 A O6 DG 17 A DG 17 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc13 A O6 DG 21 A DG 21 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc14 A O6 DG 22 A DG 22 1_555 B K K . A K 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.154 ? metalc ? metalc15 A O6 DG 22 A DG 22 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc16 A O6 DG 23 A DG 23 1_555 C K K . A K 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? hydrog TYPE_6_PAIR hydrog1 A N1 DG 3 A DG 3 1_555 A O6 DG 9 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog2 A N2 DG 3 A DG 3 1_555 A N7 DG 9 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog3 A N7 DG 3 A DG 3 1_555 A N2 DG 21 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog4 A O6 DG 3 A DG 3 1_555 A N1 DG 21 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog5 A N1 DG 4 A DG 4 1_555 A O6 DG 10 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog6 A N2 DG 4 A DG 4 1_555 A N7 DG 10 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog7 A N7 DG 4 A DG 4 1_555 A N2 DG 22 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog8 A O6 DG 4 A DG 4 1_555 A N1 DG 22 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog9 A N1 DG 5 A DG 5 1_555 A O6 DG 11 A DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog10 A N2 DG 5 A DG 5 1_555 A N7 DG 11 A DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog11 A N7 DG 5 A DG 5 1_555 A N2 DG 23 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog12 A O6 DG 5 A DG 5 1_555 A N1 DG 23 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog13 A N1 DG 9 A DG 9 1_555 A O6 DG 15 A DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog14 A N2 DG 9 A DG 9 1_555 A N7 DG 15 A DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog15 A N1 DG 10 A DG 10 1_555 A O6 DG 16 A DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog16 A N2 DG 10 A DG 10 1_555 A N7 DG 16 A DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog17 A N1 DG 11 A DG 11 1_555 A O6 DG 17 A DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog18 A N2 DG 11 A DG 11 1_555 A N7 DG 17 A DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog19 A N1 DG 15 A DG 15 1_555 A O6 DG 21 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog20 A N2 DG 15 A DG 15 1_555 A N7 DG 21 A DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog21 A N1 DG 16 A DG 16 1_555 A O6 DG 22 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog22 A N2 DG 16 A DG 16 1_555 A N7 DG 22 A DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog23 A N1 DG 17 A DG 17 1_555 A O6 DG 23 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog24 A N2 DG 17 A DG 17 1_555 A N7 DG 23 A DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C18 H24 Au N8 O4 3' _chem_comp.formula_weight 613.401 _chem_comp.id 51O _chem_comp.mon_nstd_flag . _chem_comp.name Au(caffein-2-ylidene)2 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C17 N7 51O sing 1 n n O4 C15 51O doub 2 n n N7 C15 51O sing 3 n n N7 C16 51O sing 4 n n C15 N8 51O sing 5 n n O3 C16 51O doub 6 n n C16 C13 51O sing 7 n n C18 N8 51O sing 8 n n N8 C14 51O sing 9 n n C13 C14 51O doub 10 n y C13 N5 51O sing 11 n y C14 N6 51O sing 12 n y N5 C11 51O sing 13 n n N5 C10 51O sing 14 n y N6 C12 51O sing 15 n n N6 C10 51O doub 16 n y C10 AU 51O sing 17 n n AU C1 51O sing 18 n n C1 N2 51O sing 19 n y C1 N1 51O doub 20 n y C3 N2 51O sing 21 n n N2 C5 51O sing 22 n y C2 N1 51O sing 23 n n N1 C4 51O sing 24 n y C5 C4 51O doub 25 n y C5 C6 51O sing 26 n n C4 N4 51O sing 27 n n O1 C6 51O doub 28 n n C6 N3 51O sing 29 n n N4 C8 51O sing 30 n n N4 C7 51O sing 31 n n N3 C7 51O sing 32 n n N3 C9 51O sing 33 n n C7 O2 51O doub 34 n n C17 H1 51O sing 35 n n C17 H2 51O sing 36 n n C17 H3 51O sing 37 n n C11 H4 51O sing 38 n n C11 H5 51O sing 39 n n C11 H6 51O sing 40 n n C18 H7 51O sing 41 n n C18 H8 51O sing 42 n n C18 H9 51O sing 43 n n C12 H10 51O sing 44 n n C12 H11 51O sing 45 n n C12 H12 51O sing 46 n n C3 H13 51O sing 47 n n C3 H14 51O sing 48 n n C3 H15 51O sing 49 n n C2 H16 51O sing 50 n n C2 H17 51O sing 51 n n C2 H18 51O sing 52 n n C8 H19 51O sing 53 n n C8 H20 51O sing 54 n n C8 H21 51O sing 55 n n C9 H22 51O sing 56 n n C9 H23 51O sing 57 n n C9 H24 51O sing 58 n n # _atom_sites.entry_id 5CCW _atom_sites.fract_transf_matrix[1][1] 0.021218 _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] 0.019499 _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] 0.017016 _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 K A 1 101 1 K K . C 2 K A 1 102 2 K K . D 3 51O A 1 103 1 51O NHA . E 3 51O A 1 104 2 51O NHA . F 3 51O A 1 105 3 51O NHA . G 4 HOH A 1 201 20 HOH HOH . G 4 HOH A 2 202 17 HOH HOH . G 4 HOH A 3 203 12 HOH HOH . G 4 HOH A 4 204 8 HOH HOH . G 4 HOH A 5 205 4 HOH HOH . G 4 HOH A 6 206 19 HOH HOH . G 4 HOH A 7 207 3 HOH HOH . G 4 HOH A 8 208 2 HOH HOH . G 4 HOH A 9 209 6 HOH HOH . G 4 HOH A 10 210 18 HOH HOH . G 4 HOH A 11 211 10 HOH HOH . G 4 HOH A 12 212 7 HOH HOH . G 4 HOH A 13 213 5 HOH HOH . G 4 HOH A 14 214 22 HOH HOH . G 4 HOH A 15 215 13 HOH HOH . G 4 HOH A 16 216 16 HOH HOH . G 4 HOH A 17 217 14 HOH HOH . G 4 HOH A 18 218 9 HOH HOH . G 4 HOH A 19 219 21 HOH HOH . G 4 HOH A 20 220 11 HOH HOH . G 4 HOH A 21 221 1 HOH HOH . G 4 HOH A 22 222 15 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 O O4 51O . . . F 3 -8.918 13.759 -7.53 0.5 35.05 ? O4 51O 105 A 1 HETATM 2 C C15 51O . . . F 3 -7.884 13.643 -8.168 0.5 36.58 ? C15 51O 105 A 1 HETATM 3 N N7 51O . . . F 3 -7.919 13.624 -9.567 0.5 36.36 ? N7 51O 105 A 1 HETATM 4 C C17 51O . . . F 3 -9.192 13.743 -10.272 0.5 35.52 ? C17 51O 105 A 1 HETATM 5 C C16 51O . . . F 3 -6.726 13.491 -10.286 0.5 37.31 ? C16 51O 105 A 1 HETATM 6 O O3 51O . . . F 3 -6.744 13.474 -11.506 0.5 41.31 ? O3 51O 105 A 1 HETATM 7 C C13 51O . . . F 3 -5.51 13.378 -9.6 0.5 35.61 ? C13 51O 105 A 1 HETATM 8 N N5 51O . . . F 3 -4.188 13.237 -10.031 0.5 35.47 ? N5 51O 105 A 1 HETATM 9 C C11 51O . . . F 3 -3.753 13.17 -11.424 0.5 36.21 ? C11 51O 105 A 1 HETATM 10 N N8 51O . . . F 3 -6.657 13.529 -7.506 0.5 35.58 ? N8 51O 105 A 1 HETATM 11 C C18 51O . . . F 3 -6.607 13.547 -6.047 0.5 35.45 ? C18 51O 105 A 1 HETATM 12 C C14 51O . . . F 3 -5.476 13.397 -8.247 0.5 36.18 ? C14 51O 105 A 1 HETATM 13 N N6 51O . . . F 3 -4.134 13.266 -7.878 0.5 37.09 ? N6 51O 105 A 1 HETATM 14 C C12 51O . . . F 3 -3.631 13.236 -6.508 0.5 35.46 ? C12 51O 105 A 1 HETATM 15 C C10 51O . . . F 3 -3.392 13.173 -8.973 0.5 33.64 ? C10 51O 105 A 1 HETATM 16 AU AU 51O . . . F 3 -1.383 12.967 -9.02 0.5 36.03 ? AU 51O 105 A 1 HETATM 17 C C1 51O . . . F 3 0.626 12.762 -9.067 0.5 34.46 ? C1 51O 105 A 1 HETATM 18 N N2 51O . . . F 3 1.371 12.668 -10.158 0.5 35.69 ? N2 51O 105 A 1 HETATM 19 C C5 51O . . . F 3 2.709 12.538 -9.774 0.5 33.65 ? C5 51O 105 A 1 HETATM 20 C C3 51O . . . F 3 0.877 12.696 -11.532 0.5 36.76 ? C3 51O 105 A 1 HETATM 21 N N1 51O . . . F 3 1.405 12.699 -7.998 0.5 34.2 ? N1 51O 105 A 1 HETATM 22 C C2 51O . . . F 3 0.954 12.768 -6.61 0.5 35.83 ? C2 51O 105 A 1 HETATM 23 C C4 51O . . . F 3 2.73 12.557 -8.419 0.5 33.28 ? C4 51O 105 A 1 HETATM 24 N N4 51O . . . F 3 3.94 12.445 -7.723 0.5 36.28 ? N4 51O 105 A 1 HETATM 25 C C8 51O . . . F 3 3.95 12.468 -6.263 0.5 36.22 ? C8 51O 105 A 1 HETATM 26 C C7 51O . . . F 3 5.14 12.312 -8.431 0.5 36.02 ? C7 51O 105 A 1 HETATM 27 O O2 51O . . . F 3 6.199 12.213 -7.832 0.5 35.35 ? O2 51O 105 A 1 HETATM 28 N N3 51O . . . F 3 5.118 12.291 -9.83 0.5 35.34 ? N3 51O 105 A 1 HETATM 29 C C9 51O . . . F 3 6.362 12.152 -10.582 0.5 38.19 ? C9 51O 105 A 1 HETATM 30 C C6 51O . . . F 3 3.897 12.405 -10.504 0.5 36.15 ? C6 51O 105 A 1 HETATM 31 O O1 51O . . . F 3 3.867 12.388 -11.723 0.5 37.93 ? O1 51O 105 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #