data_7C40 # _model_server_result.job_id aeTd-SJz9nKvjhJo17NrWQ _model_server_result.datetime_utc '2024-11-04 23:31:45' _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 7c40 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1002}' # _entry.id 7C40 # _exptl.entry_id 7C40 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 7C40 _cell.length_a 82.547 _cell.length_b 82.547 _cell.length_c 40.804 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7C40 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 _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 3 _struct_asym.id C _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 OG SER 17 A SER 17 1_555 B MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 B MG MG . A MG 1001 1_555 C O3B GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc3 B MG MG . A MG 1001 1_555 D O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc4 B MG MG . A MG 1001 1_555 D O HOH . A HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc5 B MG MG . A MG 1001 1_555 D O HOH . A HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 7C40 _atom_sites.fract_transf_matrix[1][1] 0.012114 _atom_sites.fract_transf_matrix[1][2] 0.006994 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013988 _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] 0.024507 _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 1001 1001 MG MG . C 3 GDP A 1 1002 1002 GDP GDP . D 4 HOH A 1 1101 1101 HOH HOH . D 4 HOH A 2 1102 1102 HOH HOH . D 4 HOH A 3 1103 1103 HOH HOH . D 4 HOH A 4 1104 1104 HOH HOH . D 4 HOH A 5 1105 1105 HOH HOH . D 4 HOH A 6 1106 1106 HOH HOH . D 4 HOH A 7 1107 1107 HOH HOH . D 4 HOH A 8 1108 1108 HOH HOH . D 4 HOH A 9 1109 1109 HOH HOH . D 4 HOH A 10 1110 1110 HOH HOH . D 4 HOH A 11 1111 1111 HOH HOH . D 4 HOH A 12 1112 1112 HOH HOH . D 4 HOH A 13 1113 1113 HOH HOH . D 4 HOH A 14 1114 1114 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 P PB GDP . . . C 3 -10.756 -35.572 -7.302 1 26.48 ? PB GDP 1002 A 1 HETATM 2 O O1B GDP . . . C 3 -9.891 -36.347 -8.255 1 24.3 ? O1B GDP 1002 A 1 HETATM 3 O O2B GDP . . . C 3 -9.873 -34.998 -6.22 1 19.21 ? O2B GDP 1002 A 1 HETATM 4 O O3B GDP . . . C 3 -11.477 -34.446 -8.033 1 28.86 ? O3B GDP 1002 A 1 HETATM 5 O O3A GDP . . . C 3 -11.795 -36.622 -6.667 1 22.87 ? O3A GDP 1002 A 1 HETATM 6 P PA GDP . . . C 3 -13.365 -36.716 -6.977 1 24.45 ? PA GDP 1002 A 1 HETATM 7 O O1A GDP . . . C 3 -13.564 -36.943 -8.466 1 20.75 ? O1A GDP 1002 A 1 HETATM 8 O O2A GDP . . . C 3 -14.129 -35.515 -6.433 1 19.94 ? O2A GDP 1002 A 1 HETATM 9 O O5' GDP . . . C 3 -13.784 -38.072 -6.22 1 19.55 ? O5' GDP 1002 A 1 HETATM 10 C C5' GDP . . . C 3 -13.175 -39.31 -6.576 1 17.23 ? C5' GDP 1002 A 1 HETATM 11 C C4' GDP . . . C 3 -14.115 -40.426 -6.136 1 20.49 ? C4' GDP 1002 A 1 HETATM 12 O O4' GDP . . . C 3 -14.217 -40.427 -4.696 1 20.47 ? O4' GDP 1002 A 1 HETATM 13 C C3' GDP . . . C 3 -15.51 -40.146 -6.668 1 25.89 ? C3' GDP 1002 A 1 HETATM 14 O O3' GDP . . . C 3 -16.037 -41.385 -7.167 1 27.97 ? O3' GDP 1002 A 1 HETATM 15 C C2' GDP . . . C 3 -16.326 -39.676 -5.474 1 24.54 ? C2' GDP 1002 A 1 HETATM 16 O O2' GDP . . . C 3 -17.683 -40.1 -5.597 1 29.92 ? O2' GDP 1002 A 1 HETATM 17 C C1' GDP . . . C 3 -15.611 -40.35 -4.304 1 20.1 ? C1' GDP 1002 A 1 HETATM 18 N N9 GDP . . . C 3 -15.676 -39.538 -3.083 1 22.04 ? N9 GDP 1002 A 1 HETATM 19 C C8 GDP . . . C 3 -15.31 -38.244 -2.964 1 21.77 ? C8 GDP 1002 A 1 HETATM 20 N N7 GDP . . . C 3 -15.467 -37.821 -1.686 1 26.05 ? N7 GDP 1002 A 1 HETATM 21 C C5 GDP . . . C 3 -15.954 -38.847 -0.963 1 26.46 ? C5 GDP 1002 A 1 HETATM 22 C C6 GDP . . . C 3 -16.328 -39.075 0.441 1 27.66 ? C6 GDP 1002 A 1 HETATM 23 O O6 GDP . . . C 3 -16.237 -38.163 1.296 1 30.94 ? O6 GDP 1002 A 1 HETATM 24 N N1 GDP . . . C 3 -16.741 -40.296 0.786 1 27.7 ? N1 GDP 1002 A 1 HETATM 25 C C2 GDP . . . C 3 -16.834 -41.317 -0.082 1 24.55 ? C2 GDP 1002 A 1 HETATM 26 N N2 GDP . . . C 3 -17.293 -42.516 0.358 1 23.22 ? N2 GDP 1002 A 1 HETATM 27 N N3 GDP . . . C 3 -16.506 -41.183 -1.378 1 26.62 ? N3 GDP 1002 A 1 HETATM 28 C C4 GDP . . . C 3 -16.062 -39.992 -1.873 1 31.2 ? C4 GDP 1002 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #