data_7YXD # _model_server_result.job_id M-0wzHWDyarRC-uLcsw9pQ _model_server_result.datetime_utc '2024-10-13 08:19:03' _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 7yxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 7YXD # _exptl.entry_id 7YXD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 392.461 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DEXAMETHASONE _entity.pdbx_number_of_molecules 4 _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 7YXD _cell.length_a 107.599 _cell.length_b 107.599 _cell.length_c 135.641 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YXD _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,N 1 1 C,D,J,O 2 1 E,F,K,L,P 3 1 G,H,M,Q 4 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 I N N ? 3 J N N ? 3 K N N ? 3 M N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id OG1 _struct_conn.ptnr1_label_comp_id THR _struct_conn.ptnr1_label_seq_id 27 _struct_conn.ptnr1_auth_asym_id H _struct_conn.ptnr1_auth_comp_id THR _struct_conn.ptnr1_auth_seq_id 555 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id L _struct_conn.ptnr2_label_atom_id NA _struct_conn.ptnr2_label_comp_id NA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id H _struct_conn.ptnr2_auth_comp_id NA _struct_conn.ptnr2_auth_seq_id 1002 _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 2.24 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C22 H29 F O5' _chem_comp.formula_weight 392.461 _chem_comp.id DEX _chem_comp.mon_nstd_flag . _chem_comp.name DEXAMETHASONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9A-FLUORO-16BETA-METHYLPREDNISOLONE # 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 DEX doub 83 n n C1 C10 DEX sing 84 n n C1 H1 DEX sing 85 n n C2 C3 DEX sing 86 n n C2 H2 DEX sing 87 n n C3 C4 DEX sing 88 n n C3 O1 DEX doub 89 n n C4 C5 DEX doub 90 n n C4 H4 DEX sing 91 n n C5 C6 DEX sing 92 n n C5 C10 DEX sing 93 n n C6 C7 DEX sing 94 n n C6 H61 DEX sing 95 n n C6 H62 DEX sing 96 n n C7 C8 DEX sing 97 n n C7 H71 DEX sing 98 n n C7 H72 DEX sing 99 n n C8 C9 DEX sing 100 n n C8 C14 DEX sing 101 n n C8 H8 DEX sing 102 n n C9 C10 DEX sing 103 n n C9 C11 DEX sing 104 n n C9 F1 DEX sing 105 n n C10 C19 DEX sing 106 n n C11 C12 DEX sing 107 n n C11 O2 DEX sing 108 n n C11 H11 DEX sing 109 n n C12 C13 DEX sing 110 n n C12 H211 DEX sing 111 n n C12 H221 DEX sing 112 n n C13 C14 DEX sing 113 n n C13 C17 DEX sing 114 n n C13 C18 DEX sing 115 n n C14 C15 DEX sing 116 n n C14 H14 DEX sing 117 n n C15 C16 DEX sing 118 n n C15 H511 DEX sing 119 n n C15 H521 DEX sing 120 n n C16 C17 DEX sing 121 n n C16 C22 DEX sing 122 n n C16 H16 DEX sing 123 n n C17 C20 DEX sing 124 n n C17 O3 DEX sing 125 n n C18 H811 DEX sing 126 n n C18 H821 DEX sing 127 n n C18 H831 DEX sing 128 n n C19 H911 DEX sing 129 n n C19 H921 DEX sing 130 n n C19 H931 DEX sing 131 n n C20 C21 DEX sing 132 n n C20 O4 DEX doub 133 n n C21 O5 DEX sing 134 n n C21 H112 DEX sing 135 n n C21 H122 DEX sing 136 n n C22 H212 DEX sing 137 n n C22 H222 DEX sing 138 n n C22 H232 DEX sing 139 n n O2 HO2 DEX sing 140 n n O3 H3 DEX sing 141 n n O5 H5 DEX sing 142 n n # _atom_sites.entry_id 7YXD _atom_sites.fract_transf_matrix[1][1] 0.009294 _atom_sites.fract_transf_matrix[1][2] 0.005366 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010732 _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] 0.007372 _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 I 3 DEX A 1 1001 1001 DEX DEX . J 3 DEX D 1 1001 1001 DEX DEX . K 3 DEX H 1 1001 1001 DEX DEX . L 4 NA H 1 1002 1501 NA NA . M 3 DEX L 1 1001 1001 DEX DEX . N 5 HOH A 1 1101 2007 HOH HOH . N 5 HOH A 2 1102 2008 HOH HOH . N 5 HOH A 3 1103 2004 HOH HOH . N 5 HOH A 4 1104 2003 HOH HOH . O 5 HOH D 1 1101 2006 HOH HOH . P 5 HOH H 1 2001 2001 HOH HOH . P 5 HOH H 2 2002 2005 HOH HOH . Q 5 HOH L 1 1101 2002 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 DEX . . . J 3 -29.271 1.182 -10.127 1 31.68 ? C1 DEX 1001 D 1 HETATM 2 C C2 DEX . . . J 3 -30.525 1.549 -9.863 1 26.18 ? C2 DEX 1001 D 1 HETATM 3 C C3 DEX . . . J 3 -30.727 2.631 -8.942 1 29.96 ? C3 DEX 1001 D 1 HETATM 4 C C4 DEX . . . J 3 -29.757 2.647 -7.863 1 27.02 ? C4 DEX 1001 D 1 HETATM 5 C C5 DEX . . . J 3 -28.561 2.058 -7.937 1 21.05 ? C5 DEX 1001 D 1 HETATM 6 C C6 DEX . . . J 3 -27.595 2.087 -6.783 1 25.66 ? C6 DEX 1001 D 1 HETATM 7 C C7 DEX . . . J 3 -27.403 0.658 -6.249 1 25.35 ? C7 DEX 1001 D 1 HETATM 8 C C8 DEX . . . J 3 -26.836 -0.24 -7.354 1 26.78 ? C8 DEX 1001 D 1 HETATM 9 C C9 DEX . . . J 3 -27.784 -0.193 -8.573 1 29.52 ? C9 DEX 1001 D 1 HETATM 10 C C10 DEX . . . J 3 -28.144 1.253 -9.121 1 26.62 ? C10 DEX 1001 D 1 HETATM 11 C C11 DEX . . . J 3 -27.545 -1.342 -9.601 1 29.41 ? C11 DEX 1001 D 1 HETATM 12 C C12 DEX . . . J 3 -27.422 -2.717 -8.897 1 26.2 ? C12 DEX 1001 D 1 HETATM 13 C C13 DEX . . . J 3 -26.348 -2.728 -7.81 1 30.65 ? C13 DEX 1001 D 1 HETATM 14 C C14 DEX . . . J 3 -26.797 -1.658 -6.799 1 31.79 ? C14 DEX 1001 D 1 HETATM 15 C C15 DEX . . . J 3 -26.02 -1.93 -5.503 1 32.52 ? C15 DEX 1001 D 1 HETATM 16 C C16 DEX . . . J 3 -25.598 -3.416 -5.543 1 36.19 ? C16 DEX 1001 D 1 HETATM 17 C C17 DEX . . . J 3 -26.237 -3.977 -6.852 1 33.89 ? C17 DEX 1001 D 1 HETATM 18 C C18 DEX . . . J 3 -24.957 -2.416 -8.381 1 30.75 ? C18 DEX 1001 D 1 HETATM 19 C C19 DEX . . . J 3 -26.98 2.056 -9.764 1 21.21 ? C19 DEX 1001 D 1 HETATM 20 C C20 DEX . . . J 3 -25.477 -5.157 -7.431 1 37.17 ? C20 DEX 1001 D 1 HETATM 21 C C21 DEX . . . J 3 -26.265 -6.193 -8.233 1 31.24 ? C21 DEX 1001 D 1 HETATM 22 C C22 DEX . . . J 3 -25.905 -4.14 -4.22 1 34.65 ? C22 DEX 1001 D 1 HETATM 23 F F1 DEX . . . J 3 -29.013 -0.53 -7.94 1 29.7 ? F1 DEX 1001 D 1 HETATM 24 O O1 DEX . . . J 3 -31.612 3.503 -9.072 1 26.81 ? O1 DEX 1001 D 1 HETATM 25 O O2 DEX . . . J 3 -26.328 -1.081 -10.302 1 28.19 ? O2 DEX 1001 D 1 HETATM 26 O O3 DEX . . . J 3 -27.529 -4.484 -6.601 1 38.17 ? O3 DEX 1001 D 1 HETATM 27 O O4 DEX . . . J 3 -24.284 -5.284 -7.24 1 40.32 ? O4 DEX 1001 D 1 HETATM 28 O O5 DEX . . . J 3 -25.63 -6.458 -9.52 1 28.9 ? O5 DEX 1001 D 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 57 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 561 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #