data_1XJ0 # _model_server_result.job_id RB_6JzueWtZPe1WQtC7w1A _model_server_result.datetime_utc '2024-11-23 03:48:30' _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 1xj0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":180}' # _entry.id 1XJ0 # _exptl.entry_id 1XJ0 _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 1XJ0 _cell.length_a 93.64 _cell.length_b 93.64 _cell.length_c 121.56 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XJ0 _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 ? _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 covale ? covale1 A C LYS 117 A LYS 117 1_555 A N CSX 118 A CSX 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale2 A C CSX 118 A CSX 118 1_555 A N ASP 119 A ASP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 B MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc2 D O2B GDP . A GDP 180 1_555 B MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc3 B MG MG . A MG 181 1_555 E O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc4 B MG MG . A MG 181 1_555 E O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc5 B MG MG . A MG 181 1_555 E O HOH . A HOH 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc6 B MG MG . A MG 181 1_555 E O HOH . A HOH 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc7 C MG MG . A MG 182 1_555 E O HOH . A HOH 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc8 C MG MG . A MG 182 1_555 E O HOH . A HOH 262 17_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc9 C MG MG . A MG 182 1_555 E O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc10 C MG MG . A MG 182 1_555 E O HOH . A HOH 265 17_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc11 C MG MG . A MG 182 1_555 E O HOH . A HOH 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.544 ? metalc ? metalc12 C MG MG . A MG 182 1_555 E O HOH . A HOH 266 17_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.545 ? metalc ? metalc13 C MG MG . A MG 182 1_555 E O HOH . A HOH 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc14 C MG MG . A MG 182 1_555 E O HOH . A HOH 267 17_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? # _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 97 n n PB O2B GDP sing 98 n n PB O3B GDP sing 99 n n PB O3A GDP sing 100 n n O2B HOB2 GDP sing 101 n n O3B HOB3 GDP sing 102 n n O3A PA GDP sing 103 n n PA O1A GDP doub 104 n n PA O2A GDP sing 105 n n PA O5' GDP sing 106 n n O2A HOA2 GDP sing 107 n n O5' C5' GDP sing 108 n n C5' C4' GDP sing 109 n n C5' H5' GDP sing 110 n n C5' "H5''" GDP sing 111 n n C4' O4' GDP sing 112 n n C4' C3' GDP sing 113 n n C4' H4' GDP sing 114 n n O4' C1' GDP sing 115 n n C3' O3' GDP sing 116 n n C3' C2' GDP sing 117 n n C3' H3' GDP sing 118 n n O3' HO3' GDP sing 119 n n C2' O2' GDP sing 120 n n C2' C1' GDP sing 121 n n C2' H2' GDP sing 122 n n O2' HO2' GDP sing 123 n n C1' N9 GDP sing 124 n n C1' H1' GDP sing 125 n n N9 C8 GDP sing 126 n y N9 C4 GDP sing 127 n y C8 N7 GDP doub 128 n y C8 H8 GDP sing 129 n n N7 C5 GDP sing 130 n y C5 C6 GDP sing 131 n n C5 C4 GDP doub 132 n y C6 O6 GDP doub 133 n n C6 N1 GDP sing 134 n n N1 C2 GDP sing 135 n n N1 HN1 GDP sing 136 n n C2 N2 GDP sing 137 n n C2 N3 GDP doub 138 n n N2 HN21 GDP sing 139 n n N2 HN22 GDP sing 140 n n N3 C4 GDP sing 141 n n # _atom_sites.entry_id 1XJ0 _atom_sites.fract_transf_matrix[1][1] 0.010679 _atom_sites.fract_transf_matrix[1][2] 0.006166 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012331 _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] 0.008226 _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 1 181 181 MG MG . C 2 MG A 1 182 182 MG MG . D 3 GDP A 1 180 180 GDP GDP . E 4 HOH A 1 201 201 HOH WAT . E 4 HOH A 2 202 202 HOH WAT . E 4 HOH A 3 203 203 HOH WAT . E 4 HOH A 4 204 204 HOH WAT . E 4 HOH A 5 205 205 HOH WAT . E 4 HOH A 6 206 206 HOH WAT . E 4 HOH A 7 207 207 HOH WAT . E 4 HOH A 8 208 208 HOH WAT . E 4 HOH A 9 209 209 HOH WAT . E 4 HOH A 10 210 210 HOH WAT . E 4 HOH A 11 211 211 HOH WAT . E 4 HOH A 12 212 212 HOH WAT . E 4 HOH A 13 213 213 HOH WAT . E 4 HOH A 14 214 214 HOH WAT . E 4 HOH A 15 215 215 HOH WAT . E 4 HOH A 16 216 216 HOH WAT . E 4 HOH A 17 217 217 HOH WAT . E 4 HOH A 18 218 218 HOH WAT . E 4 HOH A 19 219 219 HOH WAT . E 4 HOH A 20 220 220 HOH WAT . E 4 HOH A 21 221 221 HOH WAT . E 4 HOH A 22 222 222 HOH WAT . E 4 HOH A 23 223 223 HOH WAT . E 4 HOH A 24 224 224 HOH WAT . E 4 HOH A 25 225 225 HOH WAT . E 4 HOH A 26 226 226 HOH WAT . E 4 HOH A 27 227 227 HOH WAT . E 4 HOH A 28 228 228 HOH WAT . E 4 HOH A 29 229 229 HOH WAT . E 4 HOH A 30 230 230 HOH WAT . E 4 HOH A 31 231 231 HOH WAT . E 4 HOH A 32 232 232 HOH WAT . E 4 HOH A 33 233 233 HOH WAT . E 4 HOH A 34 234 234 HOH WAT . E 4 HOH A 35 235 235 HOH WAT . E 4 HOH A 36 236 236 HOH WAT . E 4 HOH A 37 237 237 HOH WAT . E 4 HOH A 38 238 238 HOH WAT . E 4 HOH A 39 239 239 HOH WAT . E 4 HOH A 40 240 240 HOH WAT . E 4 HOH A 41 241 241 HOH WAT . E 4 HOH A 42 242 242 HOH WAT . E 4 HOH A 43 243 243 HOH WAT . E 4 HOH A 44 244 244 HOH WAT . E 4 HOH A 45 245 245 HOH WAT . E 4 HOH A 46 246 246 HOH WAT . E 4 HOH A 47 247 247 HOH WAT . E 4 HOH A 48 248 248 HOH WAT . E 4 HOH A 49 249 249 HOH WAT . E 4 HOH A 50 250 250 HOH WAT . E 4 HOH A 51 251 251 HOH WAT . E 4 HOH A 52 252 252 HOH WAT . E 4 HOH A 53 253 253 HOH WAT . E 4 HOH A 54 254 254 HOH WAT . E 4 HOH A 55 255 255 HOH WAT . E 4 HOH A 56 256 256 HOH WAT . E 4 HOH A 57 257 257 HOH WAT . E 4 HOH A 58 258 258 HOH WAT . E 4 HOH A 59 259 259 HOH WAT . E 4 HOH A 60 260 260 HOH WAT . E 4 HOH A 61 261 261 HOH WAT . E 4 HOH A 62 262 262 HOH WAT . E 4 HOH A 63 263 263 HOH WAT . E 4 HOH A 64 264 264 HOH WAT . E 4 HOH A 65 265 265 HOH WAT . E 4 HOH A 66 266 266 HOH WAT . E 4 HOH A 67 267 267 HOH WAT . E 4 HOH A 68 268 268 HOH WAT . # 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 -7.643 14.366 21.846 1 29.31 ? PB GDP 180 A 1 HETATM 2 O O1B GDP . . . D 3 -6.573 14.377 22.869 1 29.4 ? O1B GDP 180 A 1 HETATM 3 O O2B GDP . . . D 3 -8.047 15.613 21.252 1 26.09 ? O2B GDP 180 A 1 HETATM 4 O O3B GDP . . . D 3 -7.242 13.367 20.743 1 30.39 ? O3B GDP 180 A 1 HETATM 5 O O3A GDP . . . D 3 -8.956 13.679 22.446 1 27.26 ? O3A GDP 180 A 1 HETATM 6 P PA GDP . . . D 3 -10.496 14.165 22.408 1 31.54 ? PA GDP 180 A 1 HETATM 7 O O1A GDP . . . D 3 -10.665 15.473 23.067 1 31.81 ? O1A GDP 180 A 1 HETATM 8 O O2A GDP . . . D 3 -10.962 13.975 21.032 1 35.65 ? O2A GDP 180 A 1 HETATM 9 O O5' GDP . . . D 3 -11.096 13.012 23.366 1 31.27 ? O5' GDP 180 A 1 HETATM 10 C C5' GDP . . . D 3 -11.018 11.632 22.972 1 30.13 ? C5' GDP 180 A 1 HETATM 11 C C4' GDP . . . D 3 -12.182 10.849 23.579 1 30.54 ? C4' GDP 180 A 1 HETATM 12 O O4' GDP . . . D 3 -12.112 10.952 25 1 31.32 ? O4' GDP 180 A 1 HETATM 13 C C3' GDP . . . D 3 -13.554 11.372 23.178 1 33.43 ? C3' GDP 180 A 1 HETATM 14 O O3' GDP . . . D 3 -14.376 10.26 22.897 1 38.28 ? O3' GDP 180 A 1 HETATM 15 C C2' GDP . . . D 3 -14.05 12.181 24.381 1 34.45 ? C2' GDP 180 A 1 HETATM 16 O O2' GDP . . . D 3 -15.482 12.225 24.557 1 41.09 ? O2' GDP 180 A 1 HETATM 17 C C1' GDP . . . D 3 -13.326 11.502 25.517 1 32.05 ? C1' GDP 180 A 1 HETATM 18 N N9 GDP . . . D 3 -12.955 12.41 26.601 1 26.7 ? N9 GDP 180 A 1 HETATM 19 C C8 GDP . . . D 3 -12.175 13.532 26.616 1 28.41 ? C8 GDP 180 A 1 HETATM 20 N N7 GDP . . . D 3 -12.041 14.102 27.771 1 27.84 ? N7 GDP 180 A 1 HETATM 21 C C5 GDP . . . D 3 -12.795 13.287 28.605 1 24.99 ? C5 GDP 180 A 1 HETATM 22 C C6 GDP . . . D 3 -13.05 13.371 30.032 1 27.36 ? C6 GDP 180 A 1 HETATM 23 O O6 GDP . . . D 3 -12.637 14.211 30.824 1 26.62 ? O6 GDP 180 A 1 HETATM 24 N N1 GDP . . . D 3 -13.886 12.316 30.49 1 28.5 ? N1 GDP 180 A 1 HETATM 25 C C2 GDP . . . D 3 -14.416 11.301 29.682 1 28.63 ? C2 GDP 180 A 1 HETATM 26 N N2 GDP . . . D 3 -15.184 10.387 30.269 1 29.7 ? N2 GDP 180 A 1 HETATM 27 N N3 GDP . . . D 3 -14.174 11.224 28.358 1 26.73 ? N3 GDP 180 A 1 HETATM 28 C C4 GDP . . . D 3 -13.365 12.241 27.891 1 28.35 ? C4 GDP 180 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #