data_9LJU # _model_server_result.job_id 8bWm2R3FoSJTyXFIb_w1OQ _model_server_result.datetime_utc '2025-08-15 07:22:20' _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 9lju # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 9LJU # _exptl.entry_id 9LJU _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 9LJU _cell.length_a 139.313 _cell.length_b 139.313 _cell.length_c 93.14 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LJU _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 metalc ? metalc1 A OD1 ASP 221 A ASP 220 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A OD1 ASP 221 A ASP 220 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc3 A O THR 222 A THR 221 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc4 A OD2 ASP 319 A ASP 318 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc5 A OD1 ASP 319 A ASP 318 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? metalc ? metalc6 A OD1 ASP 320 A ASP 319 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc7 D O1B GDP . A GDP 602 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc8 D O3A GDP . A GDP 602 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc9 D O1A GDP . A GDP 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? # _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 210 n n PB O2B GDP sing 211 n n PB O3B GDP sing 212 n n PB O3A GDP sing 213 n n O2B HOB2 GDP sing 214 n n O3B HOB3 GDP sing 215 n n O3A PA GDP sing 216 n n PA O1A GDP doub 217 n n PA O2A GDP sing 218 n n PA O5' GDP sing 219 n n O2A HOA2 GDP sing 220 n n O5' C5' GDP sing 221 n n C5' C4' GDP sing 222 n n C5' H5' GDP sing 223 n n C5' "H5''" GDP sing 224 n n C4' O4' GDP sing 225 n n C4' C3' GDP sing 226 n n C4' H4' GDP sing 227 n n O4' C1' GDP sing 228 n n C3' O3' GDP sing 229 n n C3' C2' GDP sing 230 n n C3' H3' GDP sing 231 n n O3' HO3' GDP sing 232 n n C2' O2' GDP sing 233 n n C2' C1' GDP sing 234 n n C2' H2' GDP sing 235 n n O2' HO2' GDP sing 236 n n C1' N9 GDP sing 237 n n C1' H1' GDP sing 238 n n N9 C8 GDP sing 239 n y N9 C4 GDP sing 240 n y C8 N7 GDP doub 241 n y C8 H8 GDP sing 242 n n N7 C5 GDP sing 243 n y C5 C6 GDP sing 244 n n C5 C4 GDP doub 245 n y C6 O6 GDP doub 246 n n C6 N1 GDP sing 247 n n N1 C2 GDP sing 248 n n N1 HN1 GDP sing 249 n n C2 N2 GDP sing 250 n n C2 N3 GDP doub 251 n n N2 HN21 GDP sing 252 n n N2 HN22 GDP sing 253 n n N3 C4 GDP sing 254 n n # _atom_sites.entry_id 9LJU _atom_sites.fract_transf_matrix[1][1] 0.007178 _atom_sites.fract_transf_matrix[1][2] 0.004144 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008289 _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] 0.010737 _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 C 3 FAD A 1 601 604 FAD FAD . D 4 GDP A 1 602 603 GDP GDP . E 5 MN A 1 603 3 MN MN . F 5 MN A 1 604 4 MN MN . G 6 HOH A 1 701 19 HOH HOH . G 6 HOH A 2 702 21 HOH HOH . G 6 HOH A 3 703 5 HOH HOH . G 6 HOH A 4 704 75 HOH HOH . G 6 HOH A 5 705 45 HOH HOH . G 6 HOH A 6 706 35 HOH HOH . G 6 HOH A 7 707 11 HOH HOH . G 6 HOH A 8 708 95 HOH HOH . G 6 HOH A 9 709 74 HOH HOH . G 6 HOH A 10 710 7 HOH HOH . G 6 HOH A 11 711 53 HOH HOH . G 6 HOH A 12 712 3 HOH HOH . G 6 HOH A 13 713 62 HOH HOH . G 6 HOH A 14 714 54 HOH HOH . G 6 HOH A 15 715 39 HOH HOH . G 6 HOH A 16 716 2 HOH HOH . G 6 HOH A 17 717 32 HOH HOH . G 6 HOH A 18 718 1 HOH HOH . G 6 HOH A 19 719 78 HOH HOH . G 6 HOH A 20 720 23 HOH HOH . G 6 HOH A 21 721 68 HOH HOH . G 6 HOH A 22 722 24 HOH HOH . G 6 HOH A 23 723 6 HOH HOH . G 6 HOH A 24 724 10 HOH HOH . G 6 HOH A 25 725 18 HOH HOH . G 6 HOH A 26 726 37 HOH HOH . G 6 HOH A 27 727 94 HOH HOH . G 6 HOH A 28 728 28 HOH HOH . G 6 HOH A 29 729 96 HOH HOH . G 6 HOH A 30 730 38 HOH HOH . G 6 HOH A 31 731 63 HOH HOH . G 6 HOH A 32 732 46 HOH HOH . G 6 HOH A 33 733 56 HOH HOH . G 6 HOH A 34 734 41 HOH HOH . G 6 HOH A 35 735 42 HOH HOH . G 6 HOH A 36 736 20 HOH HOH . G 6 HOH A 37 737 57 HOH HOH . G 6 HOH A 38 738 73 HOH HOH . G 6 HOH A 39 739 72 HOH HOH . G 6 HOH A 40 740 80 HOH HOH . G 6 HOH A 41 741 49 HOH HOH . G 6 HOH A 42 742 70 HOH HOH . G 6 HOH A 43 743 44 HOH HOH . G 6 HOH A 44 744 40 HOH HOH . G 6 HOH A 45 745 82 HOH HOH . G 6 HOH A 46 746 67 HOH HOH . G 6 HOH A 47 747 65 HOH HOH . G 6 HOH A 48 748 69 HOH HOH . G 6 HOH A 49 749 66 HOH HOH . G 6 HOH A 50 750 47 HOH HOH . G 6 HOH A 51 751 92 HOH HOH . G 6 HOH A 52 752 51 HOH HOH . G 6 HOH A 53 753 91 HOH HOH . G 6 HOH A 54 754 79 HOH HOH . G 6 HOH A 55 755 81 HOH HOH . G 6 HOH A 56 756 64 HOH HOH . G 6 HOH A 57 757 83 HOH HOH . G 6 HOH A 58 758 71 HOH HOH . H 6 HOH T 1 101 85 HOH HOH . H 6 HOH T 2 102 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 . . . D 4 57.236 -15.49 28.825 1 50.99 ? PB GDP 602 A 1 HETATM 2 O O1B GDP . . . D 4 57.289 -15.376 30.314 1 53.57 ? O1B GDP 602 A 1 HETATM 3 O O2B GDP . . . D 4 56.525 -14.26 28.263 1 45.42 ? O2B GDP 602 A 1 HETATM 4 O O3B GDP . . . D 4 56.524 -16.752 28.362 1 42.45 ? O3B GDP 602 A 1 HETATM 5 O O3A GDP . . . D 4 58.868 -15.598 28.636 1 48.86 ? O3A GDP 602 A 1 HETATM 6 P PA GDP . . . D 4 59.743 -15.644 27.251 1 52.51 ? PA GDP 602 A 1 HETATM 7 O O1A GDP . . . D 4 60.79 -16.739 27.292 1 56.7 ? O1A GDP 602 A 1 HETATM 8 O O2A GDP . . . D 4 58.845 -15.941 26.089 1 54.87 ? O2A GDP 602 A 1 HETATM 9 O O5' GDP . . . D 4 60.361 -14.12 27.107 1 48.22 ? O5' GDP 602 A 1 HETATM 10 C C5' GDP . . . D 4 59.831 -13.173 27.991 1 48.34 ? C5' GDP 602 A 1 HETATM 11 C C4' GDP . . . D 4 59.385 -11.885 27.228 1 47.63 ? C4' GDP 602 A 1 HETATM 12 O O4' GDP . . . D 4 60.312 -11.675 25.989 1 47.29 ? O4' GDP 602 A 1 HETATM 13 C C3' GDP . . . D 4 58.212 -11.986 26.726 1 45.62 ? C3' GDP 602 A 1 HETATM 14 O O3' GDP . . . D 4 57.142 -11.734 27.686 1 40.01 ? O3' GDP 602 A 1 HETATM 15 C C2' GDP . . . D 4 58.251 -10.799 25.572 1 43.55 ? C2' GDP 602 A 1 HETATM 16 O O2' GDP . . . D 4 58.05 -9.494 26.194 1 42.11 ? O2' GDP 602 A 1 HETATM 17 C C1' GDP . . . D 4 59.394 -10.933 24.984 1 43.94 ? C1' GDP 602 A 1 HETATM 18 N N9 GDP . . . D 4 59.063 -11.715 23.769 1 45.9 ? N9 GDP 602 A 1 HETATM 19 C C8 GDP . . . D 4 59.08 -13.066 23.709 1 43.45 ? C8 GDP 602 A 1 HETATM 20 N N7 GDP . . . D 4 58.677 -13.422 22.468 1 41.85 ? N7 GDP 602 A 1 HETATM 21 C C5 GDP . . . D 4 58.398 -12.301 21.795 1 45.68 ? C5 GDP 602 A 1 HETATM 22 C C6 GDP . . . D 4 57.903 -11.999 20.375 1 43.68 ? C6 GDP 602 A 1 HETATM 23 O O6 GDP . . . D 4 57.68 -12.882 19.617 1 43.04 ? O6 GDP 602 A 1 HETATM 24 N N1 GDP . . . D 4 57.713 -10.637 19.962 1 45.01 ? N1 GDP 602 A 1 HETATM 25 C C2 GDP . . . D 4 57.971 -9.55 20.858 1 38.51 ? C2 GDP 602 A 1 HETATM 26 N N2 GDP . . . D 4 57.779 -8.183 20.456 1 41.48 ? N2 GDP 602 A 1 HETATM 27 N N3 GDP . . . D 4 58.431 -9.832 22.193 1 40.5 ? N3 GDP 602 A 1 HETATM 28 C C4 GDP . . . D 4 58.633 -11.244 22.62 1 48.51 ? C4 GDP 602 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #