data_9EIX # _model_server_result.job_id Jf1v83A2NwilNhDD-kIwlw _model_server_result.datetime_utc '2025-07-08 00:27:39' _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 9eix # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 9EIX # _exptl.entry_id 9EIX _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 111.52 _cell.angle_gamma 90 _cell.entry_id 9EIX _cell.length_a 45.416 _cell.length_b 120.893 _cell.length_c 60.826 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EIX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,F,G _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 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 NZ LYS 244 A LYS 244 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc2 A NE2 HIS 264 A HIS 264 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 A OG1 THR 291 A THR 291 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc4 A OD1 ASP 311 A ASP 311 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc5 A NE2 HIS 502 A HIS 502 1_555 D MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc6 B MN MN . A MN 701 1_555 E O4P PGA . A PGA 704 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.58 ? metalc ? metalc7 B MN MN . A MN 701 1_555 E O1P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.092 ? metalc ? metalc8 B MN MN . A MN 701 1_555 E O3P PGA . A PGA 704 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.757 ? metalc ? metalc9 B MN MN . A MN 701 1_555 E P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.521 ? metalc ? metalc10 B MN MN . A MN 701 1_555 E O4P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.495 ? metalc ? metalc11 B MN MN . A MN 701 1_555 G O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc12 B MN MN . A MN 701 1_555 G O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc13 C MN MN . A MN 702 1_555 E O3P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.552 ? metalc ? metalc14 C MN MN . A MN 702 1_555 E O4P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.707 ? metalc ? metalc15 C MN MN . A MN 702 1_555 F O3B GDP . A GDP 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc16 C MN MN . A MN 702 1_555 G O HOH . A HOH 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? # _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 9EIX _atom_sites.fract_transf_matrix[1][1] 0.022018 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008681 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008272 _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] 0.017672 _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 MN A 1 701 700 MN MN . C 2 MN A 1 702 701 MN MN . D 2 MN A 1 703 702 MN MN . E 3 PGA A 1 704 800 PGA PGA . F 4 GDP A 1 705 900 GDP GDP . G 5 HOH A 1 801 803 HOH HOH . G 5 HOH A 2 802 802 HOH HOH . G 5 HOH A 3 803 801 HOH HOH . G 5 HOH A 4 804 5 HOH HOH . G 5 HOH A 5 805 3 HOH HOH . G 5 HOH A 6 806 12 HOH HOH . G 5 HOH A 7 807 10 HOH HOH . G 5 HOH A 8 808 1 HOH HOH . G 5 HOH A 9 809 2 HOH HOH . G 5 HOH A 10 810 4 HOH HOH . G 5 HOH A 11 811 6 HOH HOH . G 5 HOH A 12 812 9 HOH HOH . G 5 HOH A 13 813 11 HOH HOH . G 5 HOH A 14 814 7 HOH HOH . G 5 HOH A 15 815 8 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 4 4.294 1.157 15.316 1 57.61 ? PB GDP 705 A 1 HETATM 2 O O1B GDP . . . F 4 4.659 -0.295 15.115 1 55.09 ? O1B GDP 705 A 1 HETATM 3 O O2B GDP . . . F 4 3.024 1.453 14.557 1 67.41 ? O2B GDP 705 A 1 HETATM 4 O O3B GDP . . . F 4 5.415 2.038 14.82 1 45.05 ? O3B GDP 705 A 1 HETATM 5 O O3A GDP . . . F 4 4.026 1.426 16.879 1 53.11 ? O3A GDP 705 A 1 HETATM 6 P PA GDP . . . F 4 5.017 2.336 17.759 1 53.28 ? PA GDP 705 A 1 HETATM 7 O O1A GDP . . . F 4 6.395 1.722 17.832 1 51.05 ? O1A GDP 705 A 1 HETATM 8 O O2A GDP . . . F 4 5.085 3.745 17.219 1 58.36 ? O2A GDP 705 A 1 HETATM 9 O O5' GDP . . . F 4 4.299 2.312 19.198 1 47.86 ? O5' GDP 705 A 1 HETATM 10 C C5' GDP . . . F 4 3.574 3.454 19.643 1 59.1 ? C5' GDP 705 A 1 HETATM 11 C C4' GDP . . . F 4 3.323 3.35 21.139 1 62.89 ? C4' GDP 705 A 1 HETATM 12 O O4' GDP . . . F 4 3.639 2.036 21.603 1 57.44 ? O4' GDP 705 A 1 HETATM 13 C C3' GDP . . . F 4 4.21 4.317 21.903 1 70.78 ? C3' GDP 705 A 1 HETATM 14 O O3' GDP . . . F 4 3.431 5.413 22.391 1 75.74 ? O3' GDP 705 A 1 HETATM 15 C C2' GDP . . . F 4 4.787 3.521 23.056 1 66.46 ? C2' GDP 705 A 1 HETATM 16 O O2' GDP . . . F 4 4.347 4.075 24.299 1 64.71 ? O2' GDP 705 A 1 HETATM 17 C C1' GDP . . . F 4 4.257 2.104 22.89 1 54 ? C1' GDP 705 A 1 HETATM 18 N N9 GDP . . . F 4 5.378 1.135 22.981 1 56.83 ? N9 GDP 705 A 1 HETATM 19 C C8 GDP . . . F 4 6.313 0.923 22.036 1 55.64 ? C8 GDP 705 A 1 HETATM 20 N N7 GDP . . . F 4 7.197 -0.03 22.428 1 62.97 ? N7 GDP 705 A 1 HETATM 21 C C5 GDP . . . F 4 6.825 -0.449 23.652 1 56.18 ? C5 GDP 705 A 1 HETATM 22 C C6 GDP . . . F 4 7.319 -1.438 24.64 1 50.73 ? C6 GDP 705 A 1 HETATM 23 O O6 GDP . . . F 4 8.334 -2.131 24.406 1 46.49 ? O6 GDP 705 A 1 HETATM 24 N N1 GDP . . . F 4 6.645 -1.566 25.79 1 53.36 ? N1 GDP 705 A 1 HETATM 25 C C2 GDP . . . F 4 5.549 -0.834 26.07 1 54.25 ? C2 GDP 705 A 1 HETATM 26 N N2 GDP . . . F 4 4.926 -1.026 27.258 1 55.92 ? N2 GDP 705 A 1 HETATM 27 N N3 GDP . . . F 4 5.041 0.089 25.212 1 45.65 ? N3 GDP 705 A 1 HETATM 28 C C4 GDP . . . F 4 5.625 0.321 24.011 1 51.37 ? C4 GDP 705 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #