data_6U05 # _model_server_result.job_id N6xWSm-TagY7NwIcRhix9A _model_server_result.datetime_utc '2025-01-25 11:53:24' _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 6u05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 6U05 # _exptl.entry_id 6U05 _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 93.53 _cell.angle_gamma 90 _cell.entry_id 6U05 _cell.length_a 77.747 _cell.length_b 44.69 _cell.length_c 79.5 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6U05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,E _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 OG1 THR 26 A THR 426 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 B O1B GDP . A GDP 901 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 C MG MG . A MG 902 1_555 E O HOH . A HOH 1021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc4 C MG MG . A MG 902 1_555 E O HOH . A HOH 1040 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc5 C MG MG . A MG 902 1_555 E O HOH . A HOH 1064 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 C MG MG . A MG 902 1_555 E O HOH . A HOH 1070 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _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 6U05 _atom_sites.fract_transf_matrix[1][1] 0.012862 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000794 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022376 _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] 0.012603 _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 1 901 1 GDP GDP . C 3 MG A 1 902 1 MG MG . D 4 PO4 A 1 903 1 PO4 PO4 . E 5 HOH A 1 1001 151 HOH HOH . E 5 HOH A 2 1002 52 HOH HOH . E 5 HOH A 3 1003 38 HOH HOH . E 5 HOH A 4 1004 144 HOH HOH . E 5 HOH A 5 1005 39 HOH HOH . E 5 HOH A 6 1006 17 HOH HOH . E 5 HOH A 7 1007 95 HOH HOH . E 5 HOH A 8 1008 16 HOH HOH . E 5 HOH A 9 1009 43 HOH HOH . E 5 HOH A 10 1010 75 HOH HOH . E 5 HOH A 11 1011 30 HOH HOH . E 5 HOH A 12 1012 69 HOH HOH . E 5 HOH A 13 1013 147 HOH HOH . E 5 HOH A 14 1014 40 HOH HOH . E 5 HOH A 15 1015 61 HOH HOH . E 5 HOH A 16 1016 92 HOH HOH . E 5 HOH A 17 1017 99 HOH HOH . E 5 HOH A 18 1018 127 HOH HOH . E 5 HOH A 19 1019 86 HOH HOH . E 5 HOH A 20 1020 49 HOH HOH . E 5 HOH A 21 1021 6 HOH HOH . E 5 HOH A 22 1022 116 HOH HOH . E 5 HOH A 23 1023 146 HOH HOH . E 5 HOH A 24 1024 22 HOH HOH . E 5 HOH A 25 1025 7 HOH HOH . E 5 HOH A 26 1026 51 HOH HOH . E 5 HOH A 27 1027 20 HOH HOH . E 5 HOH A 28 1028 123 HOH HOH . E 5 HOH A 29 1029 104 HOH HOH . E 5 HOH A 30 1030 140 HOH HOH . E 5 HOH A 31 1031 8 HOH HOH . E 5 HOH A 32 1032 77 HOH HOH . E 5 HOH A 33 1033 89 HOH HOH . E 5 HOH A 34 1034 26 HOH HOH . E 5 HOH A 35 1035 59 HOH HOH . E 5 HOH A 36 1036 46 HOH HOH . E 5 HOH A 37 1037 96 HOH HOH . E 5 HOH A 38 1038 70 HOH HOH . E 5 HOH A 39 1039 25 HOH HOH . E 5 HOH A 40 1040 166 HOH HOH . E 5 HOH A 41 1041 71 HOH HOH . E 5 HOH A 42 1042 72 HOH HOH . E 5 HOH A 43 1043 32 HOH HOH . E 5 HOH A 44 1044 28 HOH HOH . E 5 HOH A 45 1045 35 HOH HOH . E 5 HOH A 46 1046 129 HOH HOH . E 5 HOH A 47 1047 4 HOH HOH . E 5 HOH A 48 1048 133 HOH HOH . E 5 HOH A 49 1049 148 HOH HOH . E 5 HOH A 50 1050 109 HOH HOH . E 5 HOH A 51 1051 108 HOH HOH . E 5 HOH A 52 1052 87 HOH HOH . E 5 HOH A 53 1053 65 HOH HOH . E 5 HOH A 54 1054 74 HOH HOH . E 5 HOH A 55 1055 37 HOH HOH . E 5 HOH A 56 1056 24 HOH HOH . E 5 HOH A 57 1057 53 HOH HOH . E 5 HOH A 58 1058 161 HOH HOH . E 5 HOH A 59 1059 42 HOH HOH . E 5 HOH A 60 1060 62 HOH HOH . E 5 HOH A 61 1061 98 HOH HOH . E 5 HOH A 62 1062 165 HOH HOH . E 5 HOH A 63 1063 47 HOH HOH . E 5 HOH A 64 1064 139 HOH HOH . E 5 HOH A 65 1065 14 HOH HOH . E 5 HOH A 66 1066 56 HOH HOH . E 5 HOH A 67 1067 64 HOH HOH . E 5 HOH A 68 1068 45 HOH HOH . E 5 HOH A 69 1069 103 HOH HOH . E 5 HOH A 70 1070 11 HOH HOH . E 5 HOH A 71 1071 3 HOH HOH . E 5 HOH A 72 1072 118 HOH HOH . E 5 HOH A 73 1073 5 HOH HOH . E 5 HOH A 74 1074 93 HOH HOH . E 5 HOH A 75 1075 94 HOH HOH . E 5 HOH A 76 1076 29 HOH HOH . E 5 HOH A 77 1077 19 HOH HOH . E 5 HOH A 78 1078 60 HOH HOH . E 5 HOH A 79 1079 124 HOH HOH . E 5 HOH A 80 1080 33 HOH HOH . E 5 HOH A 81 1081 36 HOH HOH . E 5 HOH A 82 1082 12 HOH HOH . E 5 HOH A 83 1083 82 HOH HOH . E 5 HOH A 84 1084 112 HOH HOH . E 5 HOH A 85 1085 85 HOH HOH . E 5 HOH A 86 1086 21 HOH HOH . E 5 HOH A 87 1087 34 HOH HOH . E 5 HOH A 88 1088 111 HOH HOH . E 5 HOH A 89 1089 88 HOH HOH . E 5 HOH A 90 1090 31 HOH HOH . E 5 HOH A 91 1091 27 HOH HOH . E 5 HOH A 92 1092 114 HOH HOH . E 5 HOH A 93 1093 135 HOH HOH . E 5 HOH A 94 1094 156 HOH HOH . E 5 HOH A 95 1095 131 HOH HOH . E 5 HOH A 96 1096 106 HOH HOH . E 5 HOH A 97 1097 142 HOH HOH . E 5 HOH A 98 1098 41 HOH HOH . E 5 HOH A 99 1099 76 HOH HOH . E 5 HOH A 100 1100 97 HOH HOH . E 5 HOH A 101 1101 55 HOH HOH . E 5 HOH A 102 1102 9 HOH HOH . E 5 HOH A 103 1103 160 HOH HOH . E 5 HOH A 104 1104 54 HOH HOH . E 5 HOH A 105 1105 79 HOH HOH . E 5 HOH A 106 1106 68 HOH HOH . E 5 HOH A 107 1107 48 HOH HOH . E 5 HOH A 108 1108 81 HOH HOH . E 5 HOH A 109 1109 137 HOH HOH . E 5 HOH A 110 1110 57 HOH HOH . E 5 HOH A 111 1111 119 HOH HOH . E 5 HOH A 112 1112 126 HOH HOH . E 5 HOH A 113 1113 50 HOH HOH . E 5 HOH A 114 1114 15 HOH HOH . E 5 HOH A 115 1115 105 HOH HOH . E 5 HOH A 116 1116 18 HOH HOH . E 5 HOH A 117 1117 83 HOH HOH . E 5 HOH A 118 1118 113 HOH HOH . E 5 HOH A 119 1119 91 HOH HOH . E 5 HOH A 120 1120 63 HOH HOH . E 5 HOH A 121 1121 44 HOH HOH . E 5 HOH A 122 1122 158 HOH HOH . E 5 HOH A 123 1123 149 HOH HOH . E 5 HOH A 124 1124 102 HOH HOH . E 5 HOH A 125 1125 125 HOH HOH . E 5 HOH A 126 1126 101 HOH HOH . E 5 HOH A 127 1127 162 HOH HOH . E 5 HOH A 128 1128 78 HOH HOH . E 5 HOH A 129 1129 84 HOH HOH . E 5 HOH A 130 1130 120 HOH HOH . E 5 HOH A 131 1131 115 HOH HOH . E 5 HOH A 132 1132 121 HOH HOH . E 5 HOH A 133 1133 136 HOH HOH . E 5 HOH A 134 1134 13 HOH HOH . E 5 HOH A 135 1135 155 HOH HOH . E 5 HOH A 136 1136 153 HOH HOH . E 5 HOH A 137 1137 130 HOH HOH . E 5 HOH A 138 1138 58 HOH HOH . E 5 HOH A 139 1139 67 HOH HOH . E 5 HOH A 140 1140 80 HOH HOH . E 5 HOH A 141 1141 150 HOH HOH . E 5 HOH A 142 1142 1 HOH HOH . E 5 HOH A 143 1143 117 HOH HOH . E 5 HOH A 144 1144 107 HOH HOH . E 5 HOH A 145 1145 2 HOH HOH . E 5 HOH A 146 1146 10 HOH HOH . E 5 HOH A 147 1147 152 HOH HOH . E 5 HOH A 148 1148 110 HOH HOH . E 5 HOH A 149 1149 73 HOH HOH . E 5 HOH A 150 1150 143 HOH HOH . E 5 HOH A 151 1151 134 HOH HOH . E 5 HOH A 152 1152 159 HOH HOH . E 5 HOH A 153 1153 154 HOH HOH . E 5 HOH A 154 1154 66 HOH HOH . E 5 HOH A 155 1155 90 HOH HOH . E 5 HOH A 156 1156 23 HOH HOH . E 5 HOH A 157 1157 122 HOH HOH . E 5 HOH A 158 1158 128 HOH HOH . E 5 HOH A 159 1159 167 HOH HOH . E 5 HOH A 160 1160 132 HOH HOH . E 5 HOH A 161 1161 138 HOH HOH . E 5 HOH A 162 1162 168 HOH HOH . E 5 HOH A 163 1163 100 HOH HOH . E 5 HOH A 164 1164 141 HOH HOH . E 5 HOH A 165 1165 164 HOH HOH . E 5 HOH A 166 1166 145 HOH HOH . E 5 HOH A 167 1167 157 HOH HOH . E 5 HOH A 168 1168 163 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 24.786 1.006 16.645 1 36.5 ? PB GDP 901 A 1 HETATM 2 O O1B GDP . . . B 2 24.852 0.292 15.336 1 37.32 ? O1B GDP 901 A 1 HETATM 3 O O2B GDP . . . B 2 24.668 2.508 16.445 1 35.68 ? O2B GDP 901 A 1 HETATM 4 O O3B GDP . . . B 2 25.956 0.69 17.549 1 28.53 ? O3B GDP 901 A 1 HETATM 5 O O3A GDP . . . B 2 23.422 0.562 17.395 1 38.61 ? O3A GDP 901 A 1 HETATM 6 P PA GDP . . . B 2 22.504 -0.647 16.921 1 29.98 ? PA GDP 901 A 1 HETATM 7 O O1A GDP . . . B 2 21.604 -0.41 15.718 1 25.47 ? O1A GDP 901 A 1 HETATM 8 O O2A GDP . . . B 2 23.335 -1.894 16.719 1 35.41 ? O2A GDP 901 A 1 HETATM 9 O O5' GDP . . . B 2 21.519 -0.835 18.193 1 35.93 ? O5' GDP 901 A 1 HETATM 10 C C5' GDP . . . B 2 22.085 -1.199 19.461 1 32.3 ? C5' GDP 901 A 1 HETATM 11 C C4' GDP . . . B 2 21.019 -1.904 20.317 1 36.68 ? C4' GDP 901 A 1 HETATM 12 O O4' GDP . . . B 2 19.917 -1.018 20.502 1 32.08 ? O4' GDP 901 A 1 HETATM 13 C C3' GDP . . . B 2 20.441 -3.115 19.619 1 37.84 ? C3' GDP 901 A 1 HETATM 14 O O3' GDP . . . B 2 20.119 -4.108 20.583 1 36.52 ? O3' GDP 901 A 1 HETATM 15 C C2' GDP . . . B 2 19.136 -2.65 19.042 1 37.97 ? C2' GDP 901 A 1 HETATM 16 O O2' GDP . . . B 2 18.176 -3.694 18.954 1 39.26 ? O2' GDP 901 A 1 HETATM 17 C C1' GDP . . . B 2 18.716 -1.64 20.066 1 34.47 ? C1' GDP 901 A 1 HETATM 18 N N9 GDP . . . B 2 17.883 -0.603 19.461 1 35.65 ? N9 GDP 901 A 1 HETATM 19 C C8 GDP . . . B 2 17.93 -0.152 18.195 1 38.58 ? C8 GDP 901 A 1 HETATM 20 N N7 GDP . . . B 2 17.017 0.835 18.016 1 41.47 ? N7 GDP 901 A 1 HETATM 21 C C5 GDP . . . B 2 16.38 1.017 19.198 1 36.76 ? C5 GDP 901 A 1 HETATM 22 C C6 GDP . . . B 2 15.315 1.902 19.716 1 32.89 ? C6 GDP 901 A 1 HETATM 23 O O6 GDP . . . B 2 14.785 2.735 18.943 1 33.16 ? O6 GDP 901 A 1 HETATM 24 N N1 GDP . . . B 2 14.95 1.774 21.011 1 38.33 ? N1 GDP 901 A 1 HETATM 25 C C2 GDP . . . B 2 15.528 0.874 21.841 1 42.04 ? C2 GDP 901 A 1 HETATM 26 N N2 GDP . . . B 2 15.115 0.793 23.138 1 34.88 ? N2 GDP 901 A 1 HETATM 27 N N3 GDP . . . B 2 16.522 0.037 21.427 1 37.34 ? N3 GDP 901 A 1 HETATM 28 C C4 GDP . . . B 2 16.97 0.072 20.148 1 37.02 ? C4 GDP 901 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #