data_6DI7 # _model_server_result.job_id HVJfCVJ6zZKvG4BPTtnzgg _model_server_result.datetime_utc '2024-10-10 07:26:04' _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 6di7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 6DI7 # _exptl.entry_id 6DI7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 6DI7 _cell.length_a 84.979 _cell.length_b 84.979 _cell.length_c 271.502 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DI7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 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 metalc ? metalc1 A OG SER 77 A SER 57 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc2 A OG1 THR 97 A THR 77 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 B O3B GDP . A GDP 1001 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc4 C MG MG . A MG 1002 1_555 D O HOH . A HOH 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? # _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 6DI7 _atom_sites.fract_transf_matrix[1][1] 0.011768 _atom_sites.fract_transf_matrix[1][2] 0.006794 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013588 _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] 0.003683 _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 GDP A 1 1001 1001 GDP GDP . C 3 MG A 1 1002 1002 MG MG . D 4 HOH A 1 1101 58 HOH HOH . D 4 HOH A 2 1102 26 HOH HOH . D 4 HOH A 3 1103 11 HOH HOH . D 4 HOH A 4 1104 68 HOH HOH . D 4 HOH A 5 1105 44 HOH HOH . D 4 HOH A 6 1106 59 HOH HOH . D 4 HOH A 7 1107 7 HOH HOH . D 4 HOH A 8 1108 32 HOH HOH . D 4 HOH A 9 1109 77 HOH HOH . D 4 HOH A 10 1110 47 HOH HOH . D 4 HOH A 11 1111 2 HOH HOH . D 4 HOH A 12 1112 30 HOH HOH . D 4 HOH A 13 1113 40 HOH HOH . D 4 HOH A 14 1114 15 HOH HOH . D 4 HOH A 15 1115 45 HOH HOH . D 4 HOH A 16 1116 1 HOH HOH . D 4 HOH A 17 1117 66 HOH HOH . D 4 HOH A 18 1118 8 HOH HOH . D 4 HOH A 19 1119 5 HOH HOH . D 4 HOH A 20 1120 56 HOH HOH . D 4 HOH A 21 1121 54 HOH HOH . D 4 HOH A 22 1122 23 HOH HOH . D 4 HOH A 23 1123 74 HOH HOH . D 4 HOH A 24 1124 9 HOH HOH . D 4 HOH A 25 1125 38 HOH HOH . D 4 HOH A 26 1126 13 HOH HOH . D 4 HOH A 27 1127 62 HOH HOH . D 4 HOH A 28 1128 22 HOH HOH . D 4 HOH A 29 1129 70 HOH HOH . D 4 HOH A 30 1130 36 HOH HOH . D 4 HOH A 31 1131 53 HOH HOH . D 4 HOH A 32 1132 35 HOH HOH . D 4 HOH A 33 1133 12 HOH HOH . D 4 HOH A 34 1134 3 HOH HOH . D 4 HOH A 35 1135 18 HOH HOH . D 4 HOH A 36 1136 57 HOH HOH . D 4 HOH A 37 1137 41 HOH HOH . D 4 HOH A 38 1138 76 HOH HOH . D 4 HOH A 39 1139 43 HOH HOH . D 4 HOH A 40 1140 51 HOH HOH . D 4 HOH A 41 1141 60 HOH HOH . D 4 HOH A 42 1142 10 HOH HOH . D 4 HOH A 43 1143 34 HOH HOH . D 4 HOH A 44 1144 14 HOH HOH . D 4 HOH A 45 1145 6 HOH HOH . D 4 HOH A 46 1146 4 HOH HOH . D 4 HOH A 47 1147 21 HOH HOH . D 4 HOH A 48 1148 33 HOH HOH . D 4 HOH A 49 1149 25 HOH HOH . D 4 HOH A 50 1150 20 HOH HOH . D 4 HOH A 51 1151 72 HOH HOH . D 4 HOH A 52 1152 64 HOH HOH . D 4 HOH A 53 1153 28 HOH HOH . D 4 HOH A 54 1154 61 HOH HOH . D 4 HOH A 55 1155 37 HOH HOH . D 4 HOH A 56 1156 69 HOH HOH . D 4 HOH A 57 1157 65 HOH HOH . D 4 HOH A 58 1158 52 HOH HOH . D 4 HOH A 59 1159 78 HOH HOH . D 4 HOH A 60 1160 24 HOH HOH . D 4 HOH A 61 1161 83 HOH HOH . D 4 HOH A 62 1162 46 HOH HOH . D 4 HOH A 63 1163 17 HOH HOH . D 4 HOH A 64 1164 55 HOH HOH . D 4 HOH A 65 1165 86 HOH HOH . D 4 HOH A 66 1166 29 HOH HOH . D 4 HOH A 67 1167 85 HOH HOH . D 4 HOH A 68 1168 80 HOH HOH . D 4 HOH A 69 1169 84 HOH HOH . D 4 HOH A 70 1170 63 HOH HOH . D 4 HOH A 71 1171 19 HOH HOH . D 4 HOH A 72 1172 82 HOH HOH . D 4 HOH A 73 1173 39 HOH HOH . D 4 HOH A 74 1174 42 HOH HOH . D 4 HOH A 75 1175 81 HOH HOH . D 4 HOH A 76 1176 27 HOH HOH . D 4 HOH A 77 1177 67 HOH HOH . D 4 HOH A 78 1178 49 HOH HOH . D 4 HOH A 79 1179 73 HOH HOH . D 4 HOH A 80 1180 16 HOH HOH . D 4 HOH A 81 1181 48 HOH HOH . D 4 HOH A 82 1182 31 HOH HOH . D 4 HOH A 83 1183 50 HOH HOH . D 4 HOH A 84 1184 79 HOH HOH . D 4 HOH A 85 1185 71 HOH HOH . D 4 HOH A 86 1186 75 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 . . . B 2 5.513 19.755 101.786 1 33.53 ? PB GDP 1001 A 1 HETATM 2 O O1B GDP . . . B 2 4.667 18.729 101.105 1 33.38 ? O1B GDP 1001 A 1 HETATM 3 O O2B GDP . . . B 2 5.109 21.188 101.427 1 31.94 ? O2B GDP 1001 A 1 HETATM 4 O O3B GDP . . . B 2 5.499 19.636 103.312 1 29.71 ? O3B GDP 1001 A 1 HETATM 5 O O3A GDP . . . B 2 7.03 19.625 101.314 1 35.55 ? O3A GDP 1001 A 1 HETATM 6 P PA GDP . . . B 2 8.422 19.237 101.981 1 38.24 ? PA GDP 1001 A 1 HETATM 7 O O1A GDP . . . B 2 8.405 17.726 102.224 1 42.48 ? O1A GDP 1001 A 1 HETATM 8 O O2A GDP . . . B 2 8.726 20.058 103.173 1 40.28 ? O2A GDP 1001 A 1 HETATM 9 O O5' GDP . . . B 2 9.442 19.489 100.78 1 34.47 ? O5' GDP 1001 A 1 HETATM 10 C C5' GDP . . . B 2 9.324 18.852 99.492 1 34.93 ? C5' GDP 1001 A 1 HETATM 11 C C4' GDP . . . B 2 10.698 18.661 98.901 1 35.48 ? C4' GDP 1001 A 1 HETATM 12 O O4' GDP . . . B 2 11.317 19.947 98.668 1 36.36 ? O4' GDP 1001 A 1 HETATM 13 C C3' GDP . . . B 2 11.68 17.859 99.759 1 36.97 ? C3' GDP 1001 A 1 HETATM 14 O O3' GDP . . . B 2 12.457 16.995 98.939 1 38.24 ? O3' GDP 1001 A 1 HETATM 15 C C2' GDP . . . B 2 12.539 18.948 100.406 1 37.51 ? C2' GDP 1001 A 1 HETATM 16 O O2' GDP . . . B 2 13.86 18.491 100.677 1 38.29 ? O2' GDP 1001 A 1 HETATM 17 C C1' GDP . . . B 2 12.585 19.989 99.292 1 37.29 ? C1' GDP 1001 A 1 HETATM 18 N N9 GDP . . . B 2 12.818 21.358 99.777 1 35.17 ? N9 GDP 1001 A 1 HETATM 19 C C8 GDP . . . B 2 12.015 22.087 100.614 1 32.44 ? C8 GDP 1001 A 1 HETATM 20 N N7 GDP . . . B 2 12.477 23.292 100.855 1 36.15 ? N7 GDP 1001 A 1 HETATM 21 C C5 GDP . . . B 2 13.658 23.357 100.133 1 33.08 ? C5 GDP 1001 A 1 HETATM 22 C C6 GDP . . . B 2 14.611 24.413 99.981 1 31.99 ? C6 GDP 1001 A 1 HETATM 23 O O6 GDP . . . B 2 14.569 25.534 100.486 1 33.03 ? O6 GDP 1001 A 1 HETATM 24 N N1 GDP . . . B 2 15.658 24.053 99.155 1 29.96 ? N1 GDP 1001 A 1 HETATM 25 C C2 GDP . . . B 2 15.794 22.837 98.539 1 30.06 ? C2 GDP 1001 A 1 HETATM 26 N N2 GDP . . . B 2 16.873 22.666 97.771 1 29.87 ? N2 GDP 1001 A 1 HETATM 27 N N3 GDP . . . B 2 14.915 21.847 98.669 1 32.02 ? N3 GDP 1001 A 1 HETATM 28 C C4 GDP . . . B 2 13.881 22.171 99.468 1 31.93 ? C4 GDP 1001 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #