data_1QG2 # _model_server_result.job_id 9_M-avA8U-jFCIjI3XbFww _model_server_result.datetime_utc '2024-12-27 02:22:53' _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 1qg2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":220}' # _entry.id 1QG2 # _exptl.entry_id 1QG2 _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 1QG2 _cell.length_a 102.32 _cell.length_b 102.32 _cell.length_c 42.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QG2 _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 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 _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 OG1 THR 24 A THR 24 1_555 B MG MG . A MG 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 C O1B GDP . A GDP 220 1_555 B MG MG . A MG 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 B MG MG . A MG 221 1_555 D O HOH . A HOH 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 B MG MG . A MG 221 1_555 D O HOH . A HOH 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc5 B MG MG . A MG 221 1_555 D O HOH . A HOH 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc6 B MG MG . A MG 221 1_555 D O HOH . A HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? # _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 1QG2 _atom_sites.fract_transf_matrix[1][1] 0.009773 _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] 0.009773 _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] 0.023764 _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 1 221 221 MG MO4 . C 3 GDP A 1 220 220 GDP GDP . D 4 HOH A 1 222 1 HOH HOH . D 4 HOH A 2 223 2 HOH HOH . D 4 HOH A 3 224 3 HOH HOH . D 4 HOH A 4 225 4 HOH HOH . D 4 HOH A 5 226 5 HOH HOH . D 4 HOH A 6 227 6 HOH HOH . D 4 HOH A 7 228 7 HOH HOH . D 4 HOH A 8 229 8 HOH HOH . D 4 HOH A 9 230 9 HOH HOH . D 4 HOH A 10 231 10 HOH HOH . D 4 HOH A 11 232 11 HOH HOH . D 4 HOH A 12 233 12 HOH HOH . D 4 HOH A 13 234 13 HOH HOH . D 4 HOH A 14 235 14 HOH HOH . D 4 HOH A 15 236 15 HOH HOH . D 4 HOH A 16 237 16 HOH HOH . D 4 HOH A 17 238 17 HOH HOH . D 4 HOH A 18 239 18 HOH HOH . D 4 HOH A 19 240 19 HOH HOH . D 4 HOH A 20 241 20 HOH HOH . D 4 HOH A 21 242 21 HOH HOH . D 4 HOH A 22 243 22 HOH HOH . D 4 HOH A 23 244 23 HOH HOH . D 4 HOH A 24 245 24 HOH HOH . D 4 HOH A 25 246 25 HOH HOH . D 4 HOH A 26 247 26 HOH HOH . D 4 HOH A 27 248 27 HOH HOH . D 4 HOH A 28 249 28 HOH HOH . D 4 HOH A 29 250 29 HOH HOH . D 4 HOH A 30 251 30 HOH HOH . D 4 HOH A 31 252 31 HOH HOH . D 4 HOH A 32 253 32 HOH HOH . D 4 HOH A 33 254 33 HOH HOH . D 4 HOH A 34 255 34 HOH HOH . D 4 HOH A 35 256 35 HOH HOH . D 4 HOH A 36 257 36 HOH HOH . D 4 HOH A 37 258 37 HOH HOH . D 4 HOH A 38 259 38 HOH HOH . D 4 HOH A 39 260 39 HOH HOH . D 4 HOH A 40 261 40 HOH HOH . D 4 HOH A 41 262 41 HOH HOH . D 4 HOH A 42 263 42 HOH HOH . D 4 HOH A 43 264 43 HOH HOH . D 4 HOH A 44 265 44 HOH HOH . D 4 HOH A 45 266 45 HOH HOH . D 4 HOH A 46 267 46 HOH HOH . D 4 HOH A 47 268 47 HOH HOH . D 4 HOH A 48 269 48 HOH HOH . D 4 HOH A 49 270 49 HOH HOH . D 4 HOH A 50 271 50 HOH HOH . D 4 HOH A 51 272 51 HOH HOH . D 4 HOH A 52 273 52 HOH HOH . D 4 HOH A 53 274 53 HOH HOH . D 4 HOH A 54 275 54 HOH HOH . D 4 HOH A 55 276 55 HOH HOH . D 4 HOH A 56 277 56 HOH HOH . D 4 HOH A 57 278 57 HOH HOH . D 4 HOH A 58 279 58 HOH HOH . D 4 HOH A 59 280 221 HOH MO4 . D 4 HOH A 60 281 221 HOH MO4 . D 4 HOH A 61 282 221 HOH MO4 . D 4 HOH A 62 283 221 HOH MO4 . # 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 32.176 56.805 10.419 1 40.15 ? PB GDP 220 A 1 HETATM 2 O O1B GDP . . . C 3 33.137 56.478 11.531 1 39.84 ? O1B GDP 220 A 1 HETATM 3 O O2B GDP . . . C 3 32.715 56.251 9.152 1 41.76 ? O2B GDP 220 A 1 HETATM 4 O O3B GDP . . . C 3 30.919 56.088 10.68 1 40.04 ? O3B GDP 220 A 1 HETATM 5 O O3A GDP . . . C 3 31.946 58.396 10.384 1 41.38 ? O3A GDP 220 A 1 HETATM 6 P PA GDP . . . C 3 32.643 59.764 10.325 1 42.97 ? PA GDP 220 A 1 HETATM 7 O O1A GDP . . . C 3 32.64 60.3 11.736 1 46.13 ? O1A GDP 220 A 1 HETATM 8 O O2A GDP . . . C 3 33.974 59.579 9.739 1 40.11 ? O2A GDP 220 A 1 HETATM 9 O O5' GDP . . . C 3 31.653 60.696 9.517 1 41.13 ? O5' GDP 220 A 1 HETATM 10 C C5' GDP . . . C 3 31.268 60.508 8.182 1 39.61 ? C5' GDP 220 A 1 HETATM 11 C C4' GDP . . . C 3 30.819 61.806 7.531 1 43.23 ? C4' GDP 220 A 1 HETATM 12 O O4' GDP . . . C 3 29.542 62.16 8.184 1 44.89 ? O4' GDP 220 A 1 HETATM 13 C C3' GDP . . . C 3 31.678 63.054 7.657 1 46.94 ? C3' GDP 220 A 1 HETATM 14 O O3' GDP . . . C 3 31.423 63.964 6.577 1 49.92 ? O3' GDP 220 A 1 HETATM 15 C C2' GDP . . . C 3 31.084 63.688 8.917 1 47.72 ? C2' GDP 220 A 1 HETATM 16 O O2' GDP . . . C 3 31.507 65.011 9.126 1 40.37 ? O2' GDP 220 A 1 HETATM 17 C C1' GDP . . . C 3 29.548 63.488 8.635 1 41.86 ? C1' GDP 220 A 1 HETATM 18 N N9 GDP . . . C 3 28.8 63.597 9.905 1 47.83 ? N9 GDP 220 A 1 HETATM 19 C C8 GDP . . . C 3 28.943 62.733 10.978 1 48.78 ? C8 GDP 220 A 1 HETATM 20 N N7 GDP . . . C 3 28.181 63.024 12.005 1 49.9 ? N7 GDP 220 A 1 HETATM 21 C C5 GDP . . . C 3 27.526 64.17 11.623 1 45.94 ? C5 GDP 220 A 1 HETATM 22 C C6 GDP . . . C 3 26.568 64.915 12.358 1 42.23 ? C6 GDP 220 A 1 HETATM 23 O O6 GDP . . . C 3 26.304 64.914 13.538 1 45.65 ? O6 GDP 220 A 1 HETATM 24 N N1 GDP . . . C 3 26.166 66.029 11.608 1 45.53 ? N1 GDP 220 A 1 HETATM 25 C C2 GDP . . . C 3 26.596 66.287 10.323 1 44.54 ? C2 GDP 220 A 1 HETATM 26 N N2 GDP . . . C 3 26.08 67.397 9.848 1 46.88 ? N2 GDP 220 A 1 HETATM 27 N N3 GDP . . . C 3 27.473 65.565 9.629 1 46.12 ? N3 GDP 220 A 1 HETATM 28 C C4 GDP . . . C 3 27.908 64.517 10.336 1 43.66 ? C4 GDP 220 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 27 _model_server_stats.element_count 28 #