data_1KAO # _model_server_result.job_id pLi6ZSq1K_gx9UcnoKCJlA _model_server_result.datetime_utc '2025-02-18 17:52:37' _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 1kao # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":170}' # _entry.id 1KAO # _exptl.entry_id 1KAO _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 106.67 _cell.angle_gamma 90 _cell.entry_id 1KAO _cell.length_a 36.826 _cell.length_b 35.315 _cell.length_c 58.356 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KAO _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 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 metalc ? metalc1 A OG SER 17 A SER 17 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc2 A O GLY 26 A GLY 26 2_545 C MG MG . A MG 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc3 A OD1 ASP 38 A ASP 38 1_555 C MG MG . A MG 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc4 B MG MG . A MG 168 1_555 D O3B GDP . A GDP 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc5 B MG MG . A MG 168 1_555 E O HOH . A HOH 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc6 B MG MG . A MG 168 1_555 E O HOH . A HOH 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc7 B MG MG . A MG 168 1_555 E O HOH . A HOH 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc8 B MG MG . A MG 168 1_555 E O HOH . A HOH 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 C MG MG . A MG 169 1_555 E O HOH . A HOH 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? metalc ? metalc10 C MG MG . A MG 169 1_555 E O HOH . A HOH 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? metalc ? metalc11 C MG MG . A MG 169 1_555 E O HOH . A HOH 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? # _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 1KAO _atom_sites.fract_transf_matrix[1][1] 0.027155 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008131 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028317 _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] 0.017888 _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 1 168 1 MG MG . C 2 MG A 1 169 2 MG MG . D 3 GDP A 1 170 1 GDP GDP . E 4 HOH A 1 171 1 HOH HOH . E 4 HOH A 2 172 2 HOH HOH . E 4 HOH A 3 173 3 HOH HOH . E 4 HOH A 4 174 4 HOH HOH . E 4 HOH A 5 175 5 HOH HOH . E 4 HOH A 6 176 6 HOH HOH . E 4 HOH A 7 177 7 HOH HOH . E 4 HOH A 8 178 8 HOH HOH . E 4 HOH A 9 179 9 HOH HOH . E 4 HOH A 10 180 10 HOH HOH . E 4 HOH A 11 181 11 HOH HOH . E 4 HOH A 12 182 12 HOH HOH . E 4 HOH A 13 183 13 HOH HOH . E 4 HOH A 14 184 14 HOH HOH . E 4 HOH A 15 185 15 HOH HOH . E 4 HOH A 16 186 16 HOH HOH . E 4 HOH A 17 187 17 HOH HOH . E 4 HOH A 18 188 18 HOH HOH . E 4 HOH A 19 189 19 HOH HOH . E 4 HOH A 20 190 20 HOH HOH . E 4 HOH A 21 191 21 HOH HOH . E 4 HOH A 22 192 22 HOH HOH . E 4 HOH A 23 193 23 HOH HOH . E 4 HOH A 24 194 24 HOH HOH . E 4 HOH A 25 195 25 HOH HOH . E 4 HOH A 26 196 26 HOH HOH . E 4 HOH A 27 197 27 HOH HOH . E 4 HOH A 28 198 28 HOH HOH . E 4 HOH A 29 199 29 HOH HOH . E 4 HOH A 30 200 30 HOH HOH . E 4 HOH A 31 201 31 HOH HOH . E 4 HOH A 32 202 32 HOH HOH . E 4 HOH A 33 203 33 HOH HOH . E 4 HOH A 34 204 34 HOH HOH . E 4 HOH A 35 205 35 HOH HOH . E 4 HOH A 36 206 36 HOH HOH . E 4 HOH A 37 207 37 HOH HOH . E 4 HOH A 38 208 38 HOH HOH . E 4 HOH A 39 209 39 HOH HOH . E 4 HOH A 40 210 40 HOH HOH . E 4 HOH A 41 211 41 HOH HOH . E 4 HOH A 42 212 42 HOH HOH . E 4 HOH A 43 213 43 HOH HOH . E 4 HOH A 44 214 44 HOH HOH . E 4 HOH A 45 215 45 HOH HOH . E 4 HOH A 46 216 46 HOH HOH . E 4 HOH A 47 217 47 HOH HOH . E 4 HOH A 48 218 48 HOH HOH . E 4 HOH A 49 219 49 HOH HOH . E 4 HOH A 50 220 50 HOH HOH . E 4 HOH A 51 221 51 HOH HOH . E 4 HOH A 52 222 52 HOH HOH . E 4 HOH A 53 223 53 HOH HOH . E 4 HOH A 54 224 54 HOH HOH . E 4 HOH A 55 225 55 HOH HOH . E 4 HOH A 56 226 56 HOH HOH . E 4 HOH A 57 227 57 HOH HOH . E 4 HOH A 58 228 58 HOH HOH . E 4 HOH A 59 229 59 HOH HOH . E 4 HOH A 60 230 60 HOH HOH . E 4 HOH A 61 231 61 HOH HOH . E 4 HOH A 62 232 62 HOH HOH . E 4 HOH A 63 233 63 HOH HOH . E 4 HOH A 64 234 64 HOH HOH . E 4 HOH A 65 235 65 HOH HOH . E 4 HOH A 66 236 66 HOH HOH . E 4 HOH A 67 237 67 HOH HOH . E 4 HOH A 68 238 68 HOH HOH . E 4 HOH A 69 239 69 HOH HOH . E 4 HOH A 70 240 70 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 -8.724 -3.253 9.23 1 3.66 ? PB GDP 170 A 1 HETATM 2 O O1B GDP . . . D 3 -9.953 -3.979 9.596 1 8.03 ? O1B GDP 170 A 1 HETATM 3 O O2B GDP . . . D 3 -8.247 -2.304 10.244 1 5.45 ? O2B GDP 170 A 1 HETATM 4 O O3B GDP . . . D 3 -7.6 -4.111 8.788 1 2.5 ? O3B GDP 170 A 1 HETATM 5 O O3A GDP . . . D 3 -9.14 -2.318 7.969 1 9.17 ? O3A GDP 170 A 1 HETATM 6 P PA GDP . . . D 3 -8.739 -2.439 6.378 1 5.5 ? PA GDP 170 A 1 HETATM 7 O O1A GDP . . . D 3 -9.348 -3.661 5.836 1 11.29 ? O1A GDP 170 A 1 HETATM 8 O O2A GDP . . . D 3 -7.303 -2.2 6.231 1 3.3 ? O2A GDP 170 A 1 HETATM 9 O O5' GDP . . . D 3 -9.508 -1.155 5.828 1 6.04 ? O5' GDP 170 A 1 HETATM 10 C C5' GDP . . . D 3 -10.942 -1.09 5.862 1 7.64 ? C5' GDP 170 A 1 HETATM 11 C C4' GDP . . . D 3 -11.515 -0.337 4.675 1 6.77 ? C4' GDP 170 A 1 HETATM 12 O O4' GDP . . . D 3 -11.062 1.037 4.744 1 9.77 ? O4' GDP 170 A 1 HETATM 13 C C3' GDP . . . D 3 -11.09 -0.872 3.318 1 9.94 ? C3' GDP 170 A 1 HETATM 14 O O3' GDP . . . D 3 -12.181 -0.544 2.45 1 8.53 ? O3' GDP 170 A 1 HETATM 15 C C2' GDP . . . D 3 -9.844 0.027 3.018 1 10.28 ? C2' GDP 170 A 1 HETATM 16 O O2' GDP . . . D 3 -9.642 0.205 1.59 1 8.14 ? O2' GDP 170 A 1 HETATM 17 C C1' GDP . . . D 3 -10.282 1.372 3.59 1 7.56 ? C1' GDP 170 A 1 HETATM 18 N N9 GDP . . . D 3 -9.11 2.181 4.016 1 4.48 ? N9 GDP 170 A 1 HETATM 19 C C8 GDP . . . D 3 -8.039 1.836 4.822 1 4.14 ? C8 GDP 170 A 1 HETATM 20 N N7 GDP . . . D 3 -7.173 2.804 5.024 1 3.29 ? N7 GDP 170 A 1 HETATM 21 C C5 GDP . . . D 3 -7.694 3.841 4.249 1 3.85 ? C5 GDP 170 A 1 HETATM 22 C C6 GDP . . . D 3 -7.24 5.144 4.036 1 4.39 ? C6 GDP 170 A 1 HETATM 23 O O6 GDP . . . D 3 -6.215 5.691 4.482 1 3.17 ? O6 GDP 170 A 1 HETATM 24 N N1 GDP . . . D 3 -8.068 5.868 3.235 1 4.55 ? N1 GDP 170 A 1 HETATM 25 C C2 GDP . . . D 3 -9.24 5.41 2.691 1 5.55 ? C2 GDP 170 A 1 HETATM 26 N N2 GDP . . . D 3 -9.926 6.236 1.92 1 6.48 ? N2 GDP 170 A 1 HETATM 27 N N3 GDP . . . D 3 -9.692 4.185 2.867 1 5.09 ? N3 GDP 170 A 1 HETATM 28 C C4 GDP . . . D 3 -8.897 3.467 3.665 1 4.22 ? C4 GDP 170 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #