data_9EIW # _model_server_result.job_id J5kGV6-tLv0UihAk7I8jdA _model_server_result.datetime_utc '2025-07-08 12:49:30' _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 9eiw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 9EIW # _exptl.entry_id 9EIW _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 111.39 _cell.angle_gamma 90 _cell.entry_id 9EIW _cell.length_a 45.128 _cell.length_b 120.194 _cell.length_c 60.551 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EIW _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc2 A NE2 HIS 264 A HIS 264 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc3 A OG1 THR 291 A THR 291 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc4 A OD1 ASP 311 A ASP 311 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc5 A OE1 GLU 607 A GLU 607 1_555 D MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc6 A OE2 GLU 607 A GLU 607 1_555 D MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc7 B MN MN . A MN 701 1_555 E O4P PGA . A PGA 704 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.702 ? metalc ? metalc8 B MN MN . A MN 701 1_555 E O1P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.244 ? metalc ? metalc9 B MN MN . A MN 701 1_555 E O4P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.777 ? metalc ? metalc10 B MN MN . A MN 701 1_555 G O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc11 B MN MN . A MN 701 1_555 G O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc12 C MN MN . A MN 702 1_555 E O3P PGA . A PGA 704 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.476 ? metalc ? metalc13 C MN MN . A MN 702 1_555 F O3B GDP . A GDP 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc14 C MN MN . A MN 702 1_555 G O HOH . A HOH 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc15 C MN MN . A MN 702 1_555 G O HOH . A HOH 834 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? # _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 9EIW _atom_sites.fract_transf_matrix[1][1] 0.022159 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008678 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00832 _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] 0.017736 _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 45 HOH HOH . G 5 HOH A 5 805 32 HOH HOH . G 5 HOH A 6 806 54 HOH HOH . G 5 HOH A 7 807 7 HOH HOH . G 5 HOH A 8 808 18 HOH HOH . G 5 HOH A 9 809 53 HOH HOH . G 5 HOH A 10 810 75 HOH HOH . G 5 HOH A 11 811 9 HOH HOH . G 5 HOH A 12 812 40 HOH HOH . G 5 HOH A 13 813 12 HOH HOH . G 5 HOH A 14 814 28 HOH HOH . G 5 HOH A 15 815 52 HOH HOH . G 5 HOH A 16 816 14 HOH HOH . G 5 HOH A 17 817 38 HOH HOH . G 5 HOH A 18 818 34 HOH HOH . G 5 HOH A 19 819 20 HOH HOH . G 5 HOH A 20 820 25 HOH HOH . G 5 HOH A 21 821 21 HOH HOH . G 5 HOH A 22 822 8 HOH HOH . G 5 HOH A 23 823 19 HOH HOH . G 5 HOH A 24 824 55 HOH HOH . G 5 HOH A 25 825 6 HOH HOH . G 5 HOH A 26 826 57 HOH HOH . G 5 HOH A 27 827 24 HOH HOH . G 5 HOH A 28 828 29 HOH HOH . G 5 HOH A 29 829 74 HOH HOH . G 5 HOH A 30 830 56 HOH HOH . G 5 HOH A 31 831 30 HOH HOH . G 5 HOH A 32 832 62 HOH HOH . G 5 HOH A 33 833 16 HOH HOH . G 5 HOH A 34 834 43 HOH HOH . G 5 HOH A 35 835 76 HOH HOH . G 5 HOH A 36 836 59 HOH HOH . G 5 HOH A 37 837 11 HOH HOH . G 5 HOH A 38 838 68 HOH HOH . G 5 HOH A 39 839 1 HOH HOH . G 5 HOH A 40 840 4 HOH HOH . G 5 HOH A 41 841 17 HOH HOH . G 5 HOH A 42 842 66 HOH HOH . G 5 HOH A 43 843 63 HOH HOH . G 5 HOH A 44 844 26 HOH HOH . G 5 HOH A 45 845 46 HOH HOH . G 5 HOH A 46 846 73 HOH HOH . G 5 HOH A 47 847 3 HOH HOH . G 5 HOH A 48 848 47 HOH HOH . G 5 HOH A 49 849 33 HOH HOH . G 5 HOH A 50 850 15 HOH HOH . G 5 HOH A 51 851 48 HOH HOH . G 5 HOH A 52 852 77 HOH HOH . G 5 HOH A 53 853 2 HOH HOH . G 5 HOH A 54 854 71 HOH HOH . G 5 HOH A 55 855 42 HOH HOH . G 5 HOH A 56 856 36 HOH HOH . G 5 HOH A 57 857 50 HOH HOH . G 5 HOH A 58 858 65 HOH HOH . G 5 HOH A 59 859 10 HOH HOH . G 5 HOH A 60 860 13 HOH HOH . G 5 HOH A 61 861 22 HOH HOH . G 5 HOH A 62 862 37 HOH HOH . G 5 HOH A 63 863 5 HOH HOH . G 5 HOH A 64 864 27 HOH HOH . G 5 HOH A 65 865 72 HOH HOH . G 5 HOH A 66 866 64 HOH HOH . G 5 HOH A 67 867 51 HOH HOH . G 5 HOH A 68 868 39 HOH HOH . G 5 HOH A 69 869 49 HOH HOH . G 5 HOH A 70 870 35 HOH HOH . G 5 HOH A 71 871 44 HOH HOH . G 5 HOH A 72 872 61 HOH HOH . G 5 HOH A 73 873 31 HOH HOH . G 5 HOH A 74 874 58 HOH HOH . G 5 HOH A 75 875 41 HOH HOH . G 5 HOH A 76 876 70 HOH HOH . G 5 HOH A 77 877 60 HOH HOH . G 5 HOH A 78 878 67 HOH HOH . G 5 HOH A 79 879 23 HOH HOH . G 5 HOH A 80 880 69 HOH HOH . G 5 HOH A 81 881 78 HOH HOH . G 5 HOH A 82 882 79 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 -4.251 -0.925 15.328 1 63.56 ? PB GDP 705 A 1 HETATM 2 O O1B GDP . . . F 4 -4.288 0.561 15.059 1 62.63 ? O1B GDP 705 A 1 HETATM 3 O O2B GDP . . . F 4 -3.026 -1.529 14.686 1 58.54 ? O2B GDP 705 A 1 HETATM 4 O O3B GDP . . . F 4 -5.497 -1.551 14.754 1 58.44 ? O3B GDP 705 A 1 HETATM 5 O O3A GDP . . . F 4 -4.152 -1.163 16.92 1 62.22 ? O3A GDP 705 A 1 HETATM 6 P PA GDP . . . F 4 -5.071 -2.225 17.716 1 56.81 ? PA GDP 705 A 1 HETATM 7 O O1A GDP . . . F 4 -6.514 -1.784 17.79 1 49.77 ? O1A GDP 705 A 1 HETATM 8 O O2A GDP . . . F 4 -4.981 -3.597 17.091 1 71.15 ? O2A GDP 705 A 1 HETATM 9 O O5' GDP . . . F 4 -4.361 -2.229 19.16 1 55.3 ? O5' GDP 705 A 1 HETATM 10 C C5' GDP . . . F 4 -3.137 -2.945 19.322 1 61.48 ? C5' GDP 705 A 1 HETATM 11 C C4' GDP . . . F 4 -2.797 -3.065 20.8 1 67.72 ? C4' GDP 705 A 1 HETATM 12 O O4' GDP . . . F 4 -3.089 -1.828 21.45 1 69.51 ? O4' GDP 705 A 1 HETATM 13 C C3' GDP . . . F 4 -3.625 -4.147 21.476 1 69.13 ? C3' GDP 705 A 1 HETATM 14 O O3' GDP . . . F 4 -2.774 -5.22 21.89 1 77.92 ? O3' GDP 705 A 1 HETATM 15 C C2' GDP . . . F 4 -4.266 -3.491 22.683 1 70.06 ? C2' GDP 705 A 1 HETATM 16 O O2' GDP . . . F 4 -3.868 -4.163 23.884 1 68.52 ? O2' GDP 705 A 1 HETATM 17 C C1' GDP . . . F 4 -3.776 -2.049 22.683 1 65.4 ? C1' GDP 705 A 1 HETATM 18 N N9 GDP . . . F 4 -4.939 -1.133 22.781 1 64.49 ? N9 GDP 705 A 1 HETATM 19 C C8 GDP . . . F 4 -5.931 -1.014 21.876 1 64.34 ? C8 GDP 705 A 1 HETATM 20 N N7 GDP . . . F 4 -6.843 -0.087 22.268 1 60.26 ? N7 GDP 705 A 1 HETATM 21 C C5 GDP . . . F 4 -6.429 0.409 23.45 1 56.69 ? C5 GDP 705 A 1 HETATM 22 C C6 GDP . . . F 4 -6.918 1.418 24.418 1 55.37 ? C6 GDP 705 A 1 HETATM 23 O O6 GDP . . . F 4 -7.978 2.048 24.206 1 54.09 ? O6 GDP 705 A 1 HETATM 24 N N1 GDP . . . F 4 -6.19 1.631 25.523 1 54.63 ? N1 GDP 705 A 1 HETATM 25 C C2 GDP . . . F 4 -5.044 0.964 25.773 1 52.71 ? C2 GDP 705 A 1 HETATM 26 N N2 GDP . . . F 4 -4.358 1.232 26.911 1 53.24 ? N2 GDP 705 A 1 HETATM 27 N N3 GDP . . . F 4 -4.541 0.03 24.931 1 57.56 ? N3 GDP 705 A 1 HETATM 28 C C4 GDP . . . F 4 -5.175 -0.283 23.78 1 57.88 ? C4 GDP 705 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #