data_1A4R # _model_server_result.job_id PMmcCwYZXX4Zj68pi-qo-A _model_server_result.datetime_utc '2024-12-02 05:38:29' _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 1a4r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":200}' # _entry.id 1A4R # _exptl.entry_id 1A4R _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 90 _cell.entry_id 1A4R _cell.length_a 98.65 _cell.length_b 98.65 _cell.length_c 104.16 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1A4R _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 105 A CYS 105 1_555 A SG CYS 188 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 105 B CYS 305 1_555 B SG CYS 188 B CYS 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 C MG MG . A MG 199 1_555 D O3B GDP . A GDP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 C MG MG . A MG 199 1_555 D O1B GDP . A GDP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc4 C MG MG . A MG 199 1_555 F O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.014 ? metalc ? metalc5 C MG MG . A MG 199 1_555 F O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.776 ? metalc ? metalc6 C MG MG . A MG 199 1_555 F O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc7 C MG MG . A MG 199 1_555 F O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? # _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 1A4R _atom_sites.fract_transf_matrix[1][1] 0.010137 _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] 0.010137 _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] 0.009601 _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 C 2 MG A 1 199 199 MG MG . D 3 GDP A 1 200 200 GDP GDP . E 4 GNH B 1 400 400 GNH GNH . F 5 HOH A 1 1000 1000 HOH HOH . F 5 HOH A 2 1001 1001 HOH HOH . F 5 HOH A 3 1002 1002 HOH HOH . F 5 HOH A 4 1003 1003 HOH HOH . F 5 HOH A 5 1004 1004 HOH HOH . F 5 HOH A 6 1005 1005 HOH HOH . F 5 HOH A 7 1006 1006 HOH HOH . F 5 HOH A 8 1007 1007 HOH HOH . F 5 HOH A 9 1008 1008 HOH HOH . F 5 HOH A 10 1009 1009 HOH HOH . F 5 HOH A 11 1010 1010 HOH HOH . F 5 HOH A 12 1011 1011 HOH HOH . F 5 HOH A 13 1012 1012 HOH HOH . F 5 HOH A 14 1013 1013 HOH HOH . F 5 HOH A 15 1014 1014 HOH HOH . F 5 HOH A 16 1016 1016 HOH HOH . F 5 HOH A 17 1017 1017 HOH HOH . F 5 HOH A 18 1018 1018 HOH HOH . F 5 HOH A 19 1019 1019 HOH HOH . F 5 HOH A 20 1020 1020 HOH HOH . F 5 HOH A 21 1021 1021 HOH HOH . F 5 HOH A 22 1022 1022 HOH HOH . F 5 HOH A 23 1023 1023 HOH HOH . F 5 HOH A 24 1024 1024 HOH HOH . F 5 HOH A 25 1026 1026 HOH HOH . F 5 HOH A 26 1027 1027 HOH HOH . F 5 HOH A 27 1031 1031 HOH HOH . F 5 HOH A 28 1032 1032 HOH HOH . F 5 HOH A 29 1033 1033 HOH HOH . F 5 HOH A 30 1034 1034 HOH HOH . F 5 HOH A 31 1035 1035 HOH HOH . F 5 HOH A 32 1036 1036 HOH HOH . F 5 HOH A 33 1037 1037 HOH HOH . F 5 HOH A 34 1038 1038 HOH HOH . F 5 HOH A 35 1040 1040 HOH HOH . F 5 HOH A 36 1041 1041 HOH HOH . F 5 HOH A 37 1042 1042 HOH HOH . F 5 HOH A 38 1043 1043 HOH HOH . F 5 HOH A 39 1044 1044 HOH HOH . F 5 HOH A 40 1045 1045 HOH HOH . F 5 HOH A 41 1046 1046 HOH HOH . F 5 HOH A 42 1047 1047 HOH HOH . F 5 HOH A 43 1048 1048 HOH HOH . F 5 HOH A 44 1049 1049 HOH HOH . F 5 HOH A 45 1050 1050 HOH HOH . F 5 HOH A 46 1051 1051 HOH HOH . F 5 HOH A 47 1052 1052 HOH HOH . F 5 HOH A 48 1053 1053 HOH HOH . G 5 HOH B 1 1015 1015 HOH HOH . G 5 HOH B 2 1025 1025 HOH HOH . G 5 HOH B 3 1028 1028 HOH HOH . G 5 HOH B 4 1029 1029 HOH HOH . G 5 HOH B 5 1030 1030 HOH HOH . G 5 HOH B 6 1039 1039 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 . . . D 3 81.405 64.471 1.227 1 38.99 ? PB GDP 200 A 1 HETATM 2 O O1B GDP . . . D 3 80.877 65.837 1.219 1 37.19 ? O1B GDP 200 A 1 HETATM 3 O O2B GDP . . . D 3 81.311 63.659 2.476 1 38.85 ? O2B GDP 200 A 1 HETATM 4 O O3B GDP . . . D 3 80.786 63.654 0.125 1 36.06 ? O3B GDP 200 A 1 HETATM 5 O O3A GDP . . . D 3 82.883 64.629 0.762 1 33.38 ? O3A GDP 200 A 1 HETATM 6 P PA GDP . . . D 3 83.613 64.616 -0.677 1 31.74 ? PA GDP 200 A 1 HETATM 7 O O1A GDP . . . D 3 83.162 65.783 -1.427 1 33.17 ? O1A GDP 200 A 1 HETATM 8 O O2A GDP . . . D 3 83.494 63.287 -1.318 1 23.71 ? O2A GDP 200 A 1 HETATM 9 O O5' GDP . . . D 3 85.053 64.854 -0.084 1 27.31 ? O5' GDP 200 A 1 HETATM 10 C C5' GDP . . . D 3 85.423 66.067 0.605 1 32.1 ? C5' GDP 200 A 1 HETATM 11 C C4' GDP . . . D 3 86.942 66.335 0.506 1 34.37 ? C4' GDP 200 A 1 HETATM 12 O O4' GDP . . . D 3 87.614 65.127 0.866 1 41.2 ? O4' GDP 200 A 1 HETATM 13 C C3' GDP . . . D 3 87.501 66.638 -0.876 1 34.5 ? C3' GDP 200 A 1 HETATM 14 O O3' GDP . . . D 3 88.561 67.58 -0.805 1 37.2 ? O3' GDP 200 A 1 HETATM 15 C C2' GDP . . . D 3 87.956 65.307 -1.41 1 33.21 ? C2' GDP 200 A 1 HETATM 16 O O2' GDP . . . D 3 88.821 65.333 -2.495 1 43.62 ? O2' GDP 200 A 1 HETATM 17 C C1' GDP . . . D 3 88.524 64.703 -0.179 1 32.28 ? C1' GDP 200 A 1 HETATM 18 N N9 GDP . . . D 3 88.567 63.21 -0.101 1 27.93 ? N9 GDP 200 A 1 HETATM 19 C C8 GDP . . . D 3 87.558 62.285 -0.235 1 29.15 ? C8 GDP 200 A 1 HETATM 20 N N7 GDP . . . D 3 87.913 61.031 -0.108 1 32.06 ? N7 GDP 200 A 1 HETATM 21 C C5 GDP . . . D 3 89.285 61.104 0.132 1 32.12 ? C5 GDP 200 A 1 HETATM 22 C C6 GDP . . . D 3 90.283 60.054 0.364 1 34.71 ? C6 GDP 200 A 1 HETATM 23 O O6 GDP . . . D 3 90.081 58.839 0.395 1 35.98 ? O6 GDP 200 A 1 HETATM 24 N N1 GDP . . . D 3 91.612 60.549 0.573 1 39.27 ? N1 GDP 200 A 1 HETATM 25 C C2 GDP . . . D 3 91.975 61.912 0.566 1 41.39 ? C2 GDP 200 A 1 HETATM 26 N N2 GDP . . . D 3 93.243 62.228 0.772 1 46.29 ? N2 GDP 200 A 1 HETATM 27 N N3 GDP . . . D 3 91.06 62.908 0.353 1 40.63 ? N3 GDP 200 A 1 HETATM 28 C C4 GDP . . . D 3 89.717 62.435 0.14 1 38.2 ? C4 GDP 200 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #