data_9LJW # _model_server_result.job_id 5m_DQmuBKrjoM5DuzJA04Q _model_server_result.datetime_utc '2025-08-15 07:21:50' _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 9ljw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 9LJW # _exptl.entry_id 9LJW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 9LJW _cell.length_a 142.606 _cell.length_b 142.606 _cell.length_c 91.63 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LJW _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I _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 4 _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 C P G 1 C G 1 1_555 G O3B FAD . C FAD 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? metalc ? metalc1 B OD2 ASP 221 A ASP 220 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc2 B O THR 222 A THR 221 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 B OD1 ASP 319 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc4 B OD2 ASP 319 A ASP 318 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc5 B OD2 ASP 320 A ASP 319 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc6 D O1A GDP . A GDP 601 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc7 D O1B GDP . A GDP 601 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? hydrog WATSON-CRICK hydrog1 A N1 G 2 T G 3 1_555 C N3 C 3 C C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 2 T G 3 1_555 C O2 C 3 C C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 2 T G 3 1_555 C N4 C 3 C C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 U 3 T U 4 1_555 C N1 A 2 C A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 U 3 T U 4 1_555 C N6 A 2 C A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 4 T C 5 1_555 C N1 G 1 C G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 4 T C 5 1_555 C O6 G 1 C G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 4 T C 5 1_555 C N2 G 1 C G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 289 n n PB O2B GDP sing 290 n n PB O3B GDP sing 291 n n PB O3A GDP sing 292 n n O2B HOB2 GDP sing 293 n n O3B HOB3 GDP sing 294 n n O3A PA GDP sing 295 n n PA O1A GDP doub 296 n n PA O2A GDP sing 297 n n PA O5' GDP sing 298 n n O2A HOA2 GDP sing 299 n n O5' C5' GDP sing 300 n n C5' C4' GDP sing 301 n n C5' H5' GDP sing 302 n n C5' "H5''" GDP sing 303 n n C4' O4' GDP sing 304 n n C4' C3' GDP sing 305 n n C4' H4' GDP sing 306 n n O4' C1' GDP sing 307 n n C3' O3' GDP sing 308 n n C3' C2' GDP sing 309 n n C3' H3' GDP sing 310 n n O3' HO3' GDP sing 311 n n C2' O2' GDP sing 312 n n C2' C1' GDP sing 313 n n C2' H2' GDP sing 314 n n O2' HO2' GDP sing 315 n n C1' N9 GDP sing 316 n n C1' H1' GDP sing 317 n n N9 C8 GDP sing 318 n y N9 C4 GDP sing 319 n y C8 N7 GDP doub 320 n y C8 H8 GDP sing 321 n n N7 C5 GDP sing 322 n y C5 C6 GDP sing 323 n n C5 C4 GDP doub 324 n y C6 O6 GDP doub 325 n n C6 N1 GDP sing 326 n n N1 C2 GDP sing 327 n n N1 HN1 GDP sing 328 n n C2 N2 GDP sing 329 n n C2 N3 GDP doub 330 n n N2 HN21 GDP sing 331 n n N2 HN22 GDP sing 332 n n N3 C4 GDP sing 333 n n # _atom_sites.entry_id 9LJW _atom_sites.fract_transf_matrix[1][1] 0.007012 _atom_sites.fract_transf_matrix[1][2] 0.004049 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008097 _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] 0.010913 _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 D 4 GDP A 1 601 603 GDP GDP . E 5 MN A 1 602 604 MN MN . F 5 MN A 1 603 605 MN MN . G 6 FAD C 1 101 604 FAD FAD . H 7 HOH A 1 701 2 HOH HOH . H 7 HOH A 2 702 6 HOH HOH . H 7 HOH A 3 703 4 HOH HOH . H 7 HOH A 4 704 5 HOH HOH . I 7 HOH C 1 201 3 HOH HOH . I 7 HOH C 2 202 1 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 4 -59.342 16.126 14.702 1 98.68 ? PB GDP 601 A 1 HETATM 2 O O1B GDP . . . D 4 -60.174 15.372 15.732 1 80.47 ? O1B GDP 601 A 1 HETATM 3 O O2B GDP . . . D 4 -58.651 17.362 15.305 1 75.39 -1 O2B GDP 601 A 1 HETATM 4 O O3B GDP . . . D 4 -58.291 15.172 14.143 1 78.66 -1 O3B GDP 601 A 1 HETATM 5 O O3A GDP . . . D 4 -60.347 16.639 13.516 1 109.81 ? O3A GDP 601 A 1 HETATM 6 P PA GDP . . . D 4 -61.695 15.892 12.965 1 106.82 ? PA GDP 601 A 1 HETATM 7 O O1A GDP . . . D 4 -62.962 16.314 13.69 1 90.43 ? O1A GDP 601 A 1 HETATM 8 O O2A GDP . . . D 4 -61.865 16.13 11.464 1 98.67 -1 O2A GDP 601 A 1 HETATM 9 O O5' GDP . . . D 4 -61.349 14.349 13.292 1 94.57 ? O5' GDP 601 A 1 HETATM 10 C C5' GDP . . . D 4 -62.334 13.318 13.203 1 89.51 ? C5' GDP 601 A 1 HETATM 11 C C4' GDP . . . D 4 -61.664 11.978 12.894 1 86.67 ? C4' GDP 601 A 1 HETATM 12 O O4' GDP . . . D 4 -62.319 11.435 11.745 1 86.55 ? O4' GDP 601 A 1 HETATM 13 C C3' GDP . . . D 4 -60.173 12.068 12.54 1 83.2 ? C3' GDP 601 A 1 HETATM 14 O O3' GDP . . . D 4 -59.277 11.824 13.63 1 81.2 ? O3' GDP 601 A 1 HETATM 15 C C2' GDP . . . D 4 -59.995 10.991 11.501 1 78.74 ? C2' GDP 601 A 1 HETATM 16 O O2' GDP . . . D 4 -59.668 9.739 12.127 1 76.29 ? O2' GDP 601 A 1 HETATM 17 C C1' GDP . . . D 4 -61.35 10.966 10.805 1 83.11 ? C1' GDP 601 A 1 HETATM 18 N N9 GDP . . . D 4 -61.216 11.889 9.643 1 83.27 ? N9 GDP 601 A 1 HETATM 19 C C8 GDP . . . D 4 -61.562 13.191 9.553 1 84.76 ? C8 GDP 601 A 1 HETATM 20 N N7 GDP . . . D 4 -61.24 13.692 8.328 1 87.94 ? N7 GDP 601 A 1 HETATM 21 C C5 GDP . . . D 4 -60.666 12.699 7.619 1 79.65 ? C5 GDP 601 A 1 HETATM 22 C C6 GDP . . . D 4 -60.085 12.512 6.274 1 77.63 ? C6 GDP 601 A 1 HETATM 23 O O6 GDP . . . D 4 -60.069 13.456 5.472 1 85.97 ? O6 GDP 601 A 1 HETATM 24 N N1 GDP . . . D 4 -59.591 11.32 5.925 1 72.68 ? N1 GDP 601 A 1 HETATM 25 C C2 GDP . . . D 4 -59.616 10.285 6.778 1 76.52 ? C2 GDP 601 A 1 HETATM 26 N N2 GDP . . . D 4 -59.119 9.077 6.423 1 75.78 ? N2 GDP 601 A 1 HETATM 27 N N3 GDP . . . D 4 -60.127 10.386 8.021 1 81.79 ? N3 GDP 601 A 1 HETATM 28 C C4 GDP . . . D 4 -60.654 11.534 8.491 1 81.08 ? C4 GDP 601 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #