data_3CON # _model_server_result.job_id rtDp3fsMbK4--bpXWeqDrw _model_server_result.datetime_utc '2024-10-19 03:37:05' _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 3con # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 3CON # _exptl.entry_id 3CON _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 120 _cell.entry_id 3CON _cell.length_a 83.061 _cell.length_b 83.061 _cell.length_c 38.907 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CON _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _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 F _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 35 A SER 17 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc2 A OD1 ASP 56 A ASP 38 1_555 D MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc3 A O GLY 66 A GLY 48 1_555 C MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc4 F O2B GDP . A GDP 201 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 B MG MG . A MG 202 1_555 O O HOH . A HOH 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 B MG MG . A MG 202 1_555 O O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc7 B MG MG . A MG 202 1_555 O O HOH . A HOH 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc8 B MG MG . A MG 202 1_555 O O HOH . A HOH 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc9 C MG MG . A MG 203 1_555 O O HOH . A HOH 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc10 C MG MG . A MG 203 1_555 O O HOH . A HOH 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc11 C MG MG . A MG 203 1_555 O O HOH . A HOH 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc12 C MG MG . A MG 203 1_555 O O HOH . A HOH 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc13 C MG MG . A MG 203 1_555 O O HOH . A HOH 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc14 D MG MG . A MG 204 1_555 O O HOH . A HOH 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc15 D MG MG . A MG 204 1_555 O O HOH . A HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc16 D MG MG . A MG 204 1_555 O O HOH . A HOH 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc17 D MG MG . A MG 204 1_555 O O HOH . A HOH 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? metalc ? metalc18 E MG MG . A MG 205 1_555 O O HOH . A HOH 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc19 E MG MG . A MG 205 1_555 O O HOH . A HOH 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? # _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 3CON _atom_sites.fract_transf_matrix[1][1] 0.012039 _atom_sites.fract_transf_matrix[1][2] 0.006951 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013902 _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] 0.025702 _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 1 202 202 MG MG . C 2 MG A 1 203 203 MG MG . D 2 MG A 1 204 204 MG MG . E 2 MG A 1 205 205 MG MG . F 3 GDP A 1 201 201 GDP GDP . G 4 UNX A 1 206 206 UNX UNX . H 4 UNX A 1 207 207 UNX UNX . I 4 UNX A 1 208 208 UNX UNX . J 4 UNX A 1 209 209 UNX UNX . K 4 UNX A 1 200 200 UNX UNX . L 4 UNX A 1 211 211 UNX UNX . M 4 UNX A 1 212 212 UNX UNX . N 4 UNX A 1 213 213 UNX UNX . O 5 HOH A 1 214 1 HOH HOH . O 5 HOH A 2 215 2 HOH HOH . O 5 HOH A 3 216 3 HOH HOH . O 5 HOH A 4 217 4 HOH HOH . O 5 HOH A 5 218 5 HOH HOH . O 5 HOH A 6 219 6 HOH HOH . O 5 HOH A 7 220 7 HOH HOH . O 5 HOH A 8 221 8 HOH HOH . O 5 HOH A 9 222 9 HOH HOH . O 5 HOH A 10 223 10 HOH HOH . O 5 HOH A 11 224 11 HOH HOH . O 5 HOH A 12 225 12 HOH HOH . O 5 HOH A 13 226 13 HOH HOH . O 5 HOH A 14 227 14 HOH HOH . O 5 HOH A 15 228 15 HOH HOH . O 5 HOH A 16 229 16 HOH HOH . O 5 HOH A 17 230 17 HOH HOH . O 5 HOH A 18 231 18 HOH HOH . O 5 HOH A 19 232 19 HOH HOH . O 5 HOH A 20 233 20 HOH HOH . O 5 HOH A 21 234 21 HOH HOH . O 5 HOH A 22 235 22 HOH HOH . O 5 HOH A 23 236 23 HOH HOH . O 5 HOH A 24 237 24 HOH HOH . O 5 HOH A 25 238 25 HOH HOH . O 5 HOH A 26 239 26 HOH HOH . O 5 HOH A 27 240 27 HOH HOH . O 5 HOH A 28 241 28 HOH HOH . O 5 HOH A 29 242 29 HOH HOH . O 5 HOH A 30 243 30 HOH HOH . O 5 HOH A 31 244 31 HOH HOH . O 5 HOH A 32 245 32 HOH HOH . O 5 HOH A 33 246 33 HOH HOH . O 5 HOH A 34 247 34 HOH HOH . O 5 HOH A 35 248 35 HOH HOH . O 5 HOH A 36 249 36 HOH HOH . O 5 HOH A 37 250 37 HOH HOH . O 5 HOH A 38 251 38 HOH HOH . O 5 HOH A 39 252 39 HOH HOH . O 5 HOH A 40 253 40 HOH HOH . O 5 HOH A 41 254 41 HOH HOH . O 5 HOH A 42 255 42 HOH HOH . O 5 HOH A 43 256 43 HOH HOH . O 5 HOH A 44 257 44 HOH HOH . O 5 HOH A 45 258 45 HOH HOH . O 5 HOH A 46 259 46 HOH HOH . O 5 HOH A 47 260 47 HOH HOH . O 5 HOH A 48 261 48 HOH HOH . O 5 HOH A 49 262 49 HOH HOH . O 5 HOH A 50 263 50 HOH HOH . O 5 HOH A 51 264 51 HOH HOH . O 5 HOH A 52 265 52 HOH HOH . O 5 HOH A 53 266 53 HOH HOH . O 5 HOH A 54 267 54 HOH HOH . O 5 HOH A 55 268 55 HOH HOH . O 5 HOH A 56 269 56 HOH HOH . O 5 HOH A 57 270 57 HOH HOH . O 5 HOH A 58 271 58 HOH HOH . O 5 HOH A 59 272 59 HOH HOH . O 5 HOH A 60 273 60 HOH HOH . O 5 HOH A 61 274 61 HOH HOH . O 5 HOH A 62 275 62 HOH HOH . O 5 HOH A 63 276 63 HOH HOH . O 5 HOH A 64 277 64 HOH HOH . O 5 HOH A 65 278 65 HOH HOH . O 5 HOH A 66 279 66 HOH HOH . O 5 HOH A 67 280 67 HOH HOH . O 5 HOH A 68 281 68 HOH HOH . O 5 HOH A 69 282 69 HOH HOH . O 5 HOH A 70 283 70 HOH HOH . O 5 HOH A 71 284 71 HOH HOH . O 5 HOH A 72 285 72 HOH HOH . O 5 HOH A 73 286 73 HOH HOH . O 5 HOH A 74 287 74 HOH HOH . O 5 HOH A 75 288 75 HOH HOH . O 5 HOH A 76 289 76 HOH HOH . O 5 HOH A 77 290 77 HOH HOH . O 5 HOH A 78 291 78 HOH HOH . O 5 HOH A 79 292 79 HOH HOH . O 5 HOH A 80 293 80 HOH HOH . O 5 HOH A 81 294 81 HOH HOH . O 5 HOH A 82 295 82 HOH HOH . O 5 HOH A 83 296 83 HOH HOH . O 5 HOH A 84 297 84 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 . . . F 3 10.593 35.974 -5.499 1 18.94 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . F 3 9.812 36.736 -6.571 1 19.08 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . F 3 11.424 34.847 -6.047 1 18.63 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . F 3 9.733 35.644 -4.293 1 17.76 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . F 3 11.653 36.987 -4.847 1 19.04 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . F 3 13.234 37.094 -5.144 1 19.04 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . F 3 13.449 37.258 -6.602 1 20.5 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . F 3 13.979 35.949 -4.459 1 19.81 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . F 3 13.598 38.433 -4.299 1 17.97 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . F 3 13.098 39.697 -4.741 1 18.28 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . F 3 14.042 40.825 -4.34 1 20.15 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . F 3 14.16 40.848 -2.925 1 19.99 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . F 3 15.446 40.611 -4.876 1 19.95 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . F 3 16.006 41.881 -5.231 1 19.25 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . F 3 16.198 39.977 -3.721 1 17.45 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . F 3 17.626 40.189 -3.706 1 20.34 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . F 3 15.504 40.651 -2.54 1 19.47 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . F 3 15.563 39.844 -1.328 1 18.96 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . F 3 15.182 38.536 -1.222 1 17.51 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . F 3 15.355 38.119 0.055 1 15.72 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . F 3 15.809 39.188 0.769 1 18.64 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . F 3 16.18 39.467 2.171 1 18.51 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . F 3 16.108 38.589 3.041 1 19.06 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . F 3 16.586 40.734 2.499 1 17 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . F 3 16.704 41.744 1.577 1 18.47 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . F 3 17.111 42.96 1.974 1 20.02 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . F 3 16.357 41.585 0.279 1 18.45 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . F 3 15.934 40.327 -0.147 1 18.24 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #