data_8YAM # _model_server_result.job_id asZcjy1hjU5rZWshqsQbBg _model_server_result.datetime_utc '2024-10-19 03:49:29' _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 8yam # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":101}' # _entry.id 8YAM # _exptl.entry_id 8YAM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 283.322 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[2-(dimethylamino)ethoxy]xanthen-9-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 90 _cell.angle_gamma 120 _cell.entry_id 8YAM _cell.length_a 115.88 _cell.length_b 115.88 _cell.length_c 58.26 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YAM _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall 'P 6c 2c' _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _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 2 _struct_asym.id B _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 covale ? covale1 A O3' U 12 A U 12 1_555 A P N 13 A N 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale2 A O3' N 13 A N 13 1_555 A P N 14 A N 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale3 A O3' N 14 A N 14 1_555 A P N 15 A N 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? covale ? covale4 A O3' N 15 A N 15 1_555 A P C 16 A C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? hydrog WATSON-CRICK hydrog1 A N3 C 1 A C 1 1_555 A N1 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 C 1 A C 1 1_555 A O6 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 C 1 A C 1 1_555 A N2 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 U 2 A U 2 1_555 A N1 A 19 A A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 U 2 A U 2 1_555 A N6 A 19 A A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 3 1_555 A N3 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 3 1_555 A O2 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 3 1_555 A N4 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 4 A G 4 1_555 A N3 C 17 A C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 4 A G 4 1_555 A O2 C 17 A C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 4 A G 4 1_555 A N4 C 17 A C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 G 5 A G 5 1_555 A N3 C 16 A C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 G 5 A G 5 1_555 A O2 C 16 A C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 G 5 A G 5 1_555 A N4 C 16 A C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog15 A N2 G 5 A G 5 1_555 A N1 A 27 A A 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog16 A N3 G 5 A G 5 1_555 A N6 A 27 A A 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog17 A N3 U 6 A U 6 1_555 A N7 A 28 A A 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog18 A O4 U 6 A U 6 1_555 A N6 A 28 A A 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog19 A N4 C 7 A C 7 1_555 A N7 G 11 A G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog20 A O2 C 7 A C 7 1_555 A N6 A 29 A A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog21 A O2 C 7 A C 7 1_555 A N4 C 30 A C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog22 A N2 G 8 A G 8 1_555 A N1 A 31 A A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog23 A N3 G 8 A G 8 1_555 A N6 A 31 A A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N3 C 9 A C 9 1_555 A N1 G 33 A G 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N4 C 9 A C 9 1_555 A O6 G 33 A G 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O2 C 9 A C 9 1_555 A N2 G 33 A G 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog27 A N3 A 10 A A 10 1_555 A N6 A 32 A A 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N1 G 11 A G 11 1_555 A N3 C 30 A C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N2 G 11 A G 11 1_555 A O2 C 30 A C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O6 G 11 A G 11 1_555 A N4 C 30 A C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog31 A O2 C 16 A C 16 1_555 A N6 A 28 A A 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog32 A O2 C 17 A C 17 1_555 A N6 A 26 A A 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C17 H17 N O3' _chem_comp.formula_weight 283.322 _chem_comp.id A1LYK _chem_comp.mon_nstd_flag . _chem_comp.name 2-[2-(dimethylamino)ethoxy]xanthen-9-one _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 C02 O01 A1LYK doub 40 n n C03 C02 A1LYK sing 41 n n C04 C03 A1LYK doub 42 n y C05 C04 A1LYK sing 43 n y C06 C05 A1LYK doub 44 n y C07 C06 A1LYK sing 45 n y C08 C07 A1LYK doub 46 n y O09 C08 A1LYK sing 47 n n C10 O09 A1LYK sing 48 n n C11 C10 A1LYK doub 49 n y C12 C11 A1LYK sing 50 n y C13 C12 A1LYK doub 51 n y C15 O14 A1LYK sing 52 n n C16 C15 A1LYK sing 53 n n N17 C16 A1LYK sing 54 n n C18 N17 A1LYK sing 55 n n C19 N17 A1LYK sing 56 n n O14 C13 A1LYK sing 57 n n C20 C13 A1LYK sing 58 n y C21 C20 A1LYK doub 59 n y C02 C11 A1LYK sing 60 n n C03 C08 A1LYK sing 61 n y C10 C21 A1LYK sing 62 n y C15 H151 A1LYK sing 63 n n C15 H152 A1LYK sing 64 n n C20 H201 A1LYK sing 65 n n C21 H211 A1LYK sing 66 n n C04 H041 A1LYK sing 67 n n C05 H051 A1LYK sing 68 n n C06 H061 A1LYK sing 69 n n C07 H071 A1LYK sing 70 n n C12 H121 A1LYK sing 71 n n C16 H161 A1LYK sing 72 n n C16 H162 A1LYK sing 73 n n C18 H181 A1LYK sing 74 n n C18 H183 A1LYK sing 75 n n C18 H182 A1LYK sing 76 n n C19 H193 A1LYK sing 77 n n C19 H191 A1LYK sing 78 n n C19 H192 A1LYK sing 79 n n # _atom_sites.entry_id 8YAM _atom_sites.fract_transf_matrix[1][1] 0.00863 _atom_sites.fract_transf_matrix[1][2] 0.004982 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009965 _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] 0.017164 _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 A1LYK A 1 101 1 A1LYK LIG . C 3 HOH A 1 201 8 HOH HOH . C 3 HOH A 2 202 13 HOH HOH . C 3 HOH A 3 203 7 HOH HOH . C 3 HOH A 4 204 12 HOH HOH . C 3 HOH A 5 205 14 HOH HOH . C 3 HOH A 6 206 15 HOH HOH . C 3 HOH A 7 207 10 HOH HOH . C 3 HOH A 8 208 11 HOH HOH . C 3 HOH A 9 209 1 HOH HOH . C 3 HOH A 10 210 3 HOH HOH . C 3 HOH A 11 211 9 HOH HOH . C 3 HOH A 12 212 5 HOH HOH . C 3 HOH A 13 213 4 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 C10 A1LYK . . . B 2 50.438 -14.78 -5.766 1 50.89 ? C10 A1LYK 101 A 1 HETATM 2 C C13 A1LYK . . . B 2 52.347 -16.027 -4.149 1 57.09 ? C13 A1LYK 101 A 1 HETATM 3 C C15 A1LYK . . . B 2 54.568 -16.048 -3.254 1 91 ? C15 A1LYK 101 A 1 HETATM 4 C C20 A1LYK . . . B 2 51.018 -15.98 -3.728 1 56.12 ? C20 A1LYK 101 A 1 HETATM 5 C C21 A1LYK . . . B 2 50.061 -15.36 -4.526 1 53.08 ? C21 A1LYK 101 A 1 HETATM 6 C C02 A1LYK . . . B 2 52.116 -14.225 -7.457 1 51.85 ? C02 A1LYK 101 A 1 HETATM 7 C C03 A1LYK . . . B 2 51.122 -13.589 -8.296 1 49.25 ? C03 A1LYK 101 A 1 HETATM 8 C C04 A1LYK . . . B 2 51.516 -13.019 -9.54 1 58.6 ? C04 A1LYK 101 A 1 HETATM 9 C C05 A1LYK . . . B 2 50.561 -12.409 -10.354 1 59.27 ? C05 A1LYK 101 A 1 HETATM 10 C C06 A1LYK . . . B 2 49.22 -12.355 -9.96 1 60.35 ? C06 A1LYK 101 A 1 HETATM 11 C C07 A1LYK . . . B 2 48.845 -12.924 -8.743 1 60.52 ? C07 A1LYK 101 A 1 HETATM 12 C C08 A1LYK . . . B 2 49.821 -13.539 -7.904 1 52.73 ? C08 A1LYK 101 A 1 HETATM 13 C C11 A1LYK . . . B 2 51.731 -14.817 -6.182 1 46.23 ? C11 A1LYK 101 A 1 HETATM 14 C C12 A1LYK . . . B 2 52.712 -15.447 -5.369 1 56.12 ? C12 A1LYK 101 A 1 HETATM 15 C C16 A1LYK . . . B 2 55.668 -17.006 -2.762 1 102.49 ? C16 A1LYK 101 A 1 HETATM 16 C C18 A1LYK . . . B 2 54.644 -17.626 -0.647 1 117.88 ? C18 A1LYK 101 A 1 HETATM 17 C C19 A1LYK . . . B 2 56.315 -18.986 -1.596 1 118.48 ? C19 A1LYK 101 A 1 HETATM 18 N N17 A1LYK . . . B 2 55.204 -18.1 -1.902 1 116.4 ? N17 A1LYK 101 A 1 HETATM 19 O O01 A1LYK . . . B 2 53.246 -14.264 -7.826 1 62.19 ? O01 A1LYK 101 A 1 HETATM 20 O O09 A1LYK . . . B 2 49.377 -14.134 -6.596 1 52.22 ? O09 A1LYK 101 A 1 HETATM 21 O O14 A1LYK . . . B 2 53.302 -16.66 -3.327 1 68.39 ? O14 A1LYK 101 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #