data_8FVD # _model_server_result.job_id jHIHr-Pu9YPRxaZaIbN9gA _model_server_result.datetime_utc '2024-11-05 06:57:38' _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 8fvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 8FVD # _exptl.entry_id 8FVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 503.138 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)" _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 8FVD _cell.length_a 161.069 _cell.length_b 110.013 _cell.length_c 129.511 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -161.069 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 D O1B GTF . A GTF 602 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc2 D O2A GTF . A GTF 602 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 D O3G GTF . A GTF 602 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc4 F O1A GTF . B GTF 701 1_555 G MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc5 F O2B GTF . B GTF 701 1_555 G MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc6 F O2G GTF . B GTF 701 1_555 G MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc7 G MG MG . B MG 702 1_555 J O HOH . B HOH 813 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _chem_comp.formula 'C9 H14 F2 N3 O13 P3' _chem_comp.formula_weight 503.138 _chem_comp.id GTF _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Gemcitabine-TRIPHOSPHATE # 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 O3G PG GTF doub 129 n n O1G PG GTF sing 130 n n PG O2G GTF sing 131 n n PG O3B GTF sing 132 n n O3B PB GTF sing 133 n n O1B PB GTF doub 134 n n F2 C2' GTF sing 135 n n C3' O3' GTF sing 136 n n C3' C2' GTF sing 137 n n C3' C4' GTF sing 138 n n O2A PA GTF doub 139 n n PB O2B GTF sing 140 n n PB O3A GTF sing 141 n n C5' C4' GTF sing 142 n n C5' O5' GTF sing 143 n n F1 C2' GTF sing 144 n n C2' C1' GTF sing 145 n n C4' O4' GTF sing 146 n n O5' PA GTF sing 147 n n PA O3A GTF sing 148 n n PA O1A GTF sing 149 n n C1' O4' GTF sing 150 n n C1' N1 GTF sing 151 n n C6 N1 GTF sing 152 n n C6 C5 GTF doub 153 n n N1 C2 GTF sing 154 n n C5 C4 GTF sing 155 n n C2 O2 GTF doub 156 n n C2 N3 GTF sing 157 n n C4 N3 GTF doub 158 n n C4 N4 GTF sing 159 n n N4 H1 GTF sing 160 n n N4 H2 GTF sing 161 n n C5 H3 GTF sing 162 n n C6 H4 GTF sing 163 n n C1' H5 GTF sing 164 n n O1A H6 GTF sing 165 n n O1G H7 GTF sing 166 n n O2B H8 GTF sing 167 n n O2G H9 GTF sing 168 n n C3' H10 GTF sing 169 n n O3' H11 GTF sing 170 n n C4' H12 GTF sing 171 n n C5' H13 GTF sing 172 n n C5' H14 GTF sing 173 n n # _atom_sites.entry_id 8FVD _atom_sites.fract_transf_matrix[1][1] 0.006209 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00909 _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] 0.007721 _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 2 MLA A 1 601 601 MLA MLA . D 3 GTF A 1 602 701 GTF GTF . E 4 MG A 1 603 801 MG MG . F 3 GTF B 1 701 701 GTF GTF . G 4 MG B 1 702 801 MG MG . H 2 MLA B 1 703 601 MLA MLA . I 5 HOH A 1 701 26 HOH HOH . I 5 HOH A 2 702 225 HOH HOH . I 5 HOH A 3 703 19 HOH HOH . I 5 HOH A 4 704 227 HOH HOH . I 5 HOH A 5 705 81 HOH HOH . I 5 HOH A 6 706 201 HOH HOH . I 5 HOH A 7 707 106 HOH HOH . I 5 HOH A 8 708 85 HOH HOH . I 5 HOH A 9 709 72 HOH HOH . I 5 HOH A 10 710 14 HOH HOH . I 5 HOH A 11 711 121 HOH HOH . I 5 HOH A 12 712 138 HOH HOH . I 5 HOH A 13 713 223 HOH HOH . I 5 HOH A 14 714 215 HOH HOH . I 5 HOH A 15 715 118 HOH HOH . I 5 HOH A 16 716 112 HOH HOH . I 5 HOH A 17 717 96 HOH HOH . I 5 HOH A 18 718 30 HOH HOH . I 5 HOH A 19 719 191 HOH HOH . I 5 HOH A 20 720 202 HOH HOH . I 5 HOH A 21 721 147 HOH HOH . I 5 HOH A 22 722 115 HOH HOH . I 5 HOH A 23 723 20 HOH HOH . I 5 HOH A 24 724 6 HOH HOH . I 5 HOH A 25 725 160 HOH HOH . I 5 HOH A 26 726 140 HOH HOH . I 5 HOH A 27 727 69 HOH HOH . I 5 HOH A 28 728 5 HOH HOH . I 5 HOH A 29 729 80 HOH HOH . I 5 HOH A 30 730 88 HOH HOH . I 5 HOH A 31 731 40 HOH HOH . I 5 HOH A 32 732 39 HOH HOH . I 5 HOH A 33 733 130 HOH HOH . I 5 HOH A 34 734 210 HOH HOH . I 5 HOH A 35 735 36 HOH HOH . I 5 HOH A 36 736 8 HOH HOH . I 5 HOH A 37 737 68 HOH HOH . I 5 HOH A 38 738 28 HOH HOH . I 5 HOH A 39 739 169 HOH HOH . I 5 HOH A 40 740 180 HOH HOH . I 5 HOH A 41 741 51 HOH HOH . I 5 HOH A 42 742 181 HOH HOH . I 5 HOH A 43 743 54 HOH HOH . I 5 HOH A 44 744 157 HOH HOH . I 5 HOH A 45 745 101 HOH HOH . I 5 HOH A 46 746 92 HOH HOH . I 5 HOH A 47 747 175 HOH HOH . I 5 HOH A 48 748 63 HOH HOH . I 5 HOH A 49 749 13 HOH HOH . I 5 HOH A 50 750 103 HOH HOH . I 5 HOH A 51 751 163 HOH HOH . I 5 HOH A 52 752 87 HOH HOH . I 5 HOH A 53 753 29 HOH HOH . I 5 HOH A 54 754 212 HOH HOH . I 5 HOH A 55 755 9 HOH HOH . I 5 HOH A 56 756 220 HOH HOH . I 5 HOH A 57 757 24 HOH HOH . I 5 HOH A 58 758 52 HOH HOH . I 5 HOH A 59 759 135 HOH HOH . I 5 HOH A 60 760 77 HOH HOH . I 5 HOH A 61 761 59 HOH HOH . I 5 HOH A 62 762 133 HOH HOH . I 5 HOH A 63 763 113 HOH HOH . I 5 HOH A 64 764 78 HOH HOH . I 5 HOH A 65 765 162 HOH HOH . I 5 HOH A 66 766 43 HOH HOH . I 5 HOH A 67 767 122 HOH HOH . I 5 HOH A 68 768 170 HOH HOH . I 5 HOH A 69 769 42 HOH HOH . I 5 HOH A 70 770 204 HOH HOH . I 5 HOH A 71 771 177 HOH HOH . I 5 HOH A 72 772 12 HOH HOH . I 5 HOH A 73 773 73 HOH HOH . I 5 HOH A 74 774 185 HOH HOH . I 5 HOH A 75 775 111 HOH HOH . I 5 HOH A 76 776 134 HOH HOH . I 5 HOH A 77 777 91 HOH HOH . I 5 HOH A 78 778 195 HOH HOH . I 5 HOH A 79 779 84 HOH HOH . I 5 HOH A 80 780 114 HOH HOH . I 5 HOH A 81 781 23 HOH HOH . I 5 HOH A 82 782 167 HOH HOH . I 5 HOH A 83 783 99 HOH HOH . I 5 HOH A 84 784 150 HOH HOH . I 5 HOH A 85 785 159 HOH HOH . I 5 HOH A 86 786 67 HOH HOH . I 5 HOH A 87 787 108 HOH HOH . I 5 HOH A 88 788 110 HOH HOH . I 5 HOH A 89 789 192 HOH HOH . I 5 HOH A 90 790 221 HOH HOH . I 5 HOH A 91 791 149 HOH HOH . I 5 HOH A 92 792 151 HOH HOH . I 5 HOH A 93 793 193 HOH HOH . I 5 HOH A 94 794 194 HOH HOH . I 5 HOH A 95 795 187 HOH HOH . J 5 HOH B 1 801 144 HOH HOH . J 5 HOH B 2 802 132 HOH HOH . J 5 HOH B 3 803 136 HOH HOH . J 5 HOH B 4 804 155 HOH HOH . J 5 HOH B 5 805 1 HOH HOH . J 5 HOH B 6 806 3 HOH HOH . J 5 HOH B 7 807 21 HOH HOH . J 5 HOH B 8 808 217 HOH HOH . J 5 HOH B 9 809 205 HOH HOH . J 5 HOH B 10 810 203 HOH HOH . J 5 HOH B 11 811 98 HOH HOH . J 5 HOH B 12 812 116 HOH HOH . J 5 HOH B 13 813 226 HOH HOH . J 5 HOH B 14 814 154 HOH HOH . J 5 HOH B 15 815 183 HOH HOH . J 5 HOH B 16 816 4 HOH HOH . J 5 HOH B 17 817 184 HOH HOH . J 5 HOH B 18 818 166 HOH HOH . J 5 HOH B 19 819 27 HOH HOH . J 5 HOH B 20 820 131 HOH HOH . J 5 HOH B 21 821 76 HOH HOH . J 5 HOH B 22 822 75 HOH HOH . J 5 HOH B 23 823 2 HOH HOH . J 5 HOH B 24 824 100 HOH HOH . J 5 HOH B 25 825 218 HOH HOH . J 5 HOH B 26 826 49 HOH HOH . J 5 HOH B 27 827 105 HOH HOH . J 5 HOH B 28 828 61 HOH HOH . J 5 HOH B 29 829 34 HOH HOH . J 5 HOH B 30 830 213 HOH HOH . J 5 HOH B 31 831 216 HOH HOH . J 5 HOH B 32 832 206 HOH HOH . J 5 HOH B 33 833 90 HOH HOH . J 5 HOH B 34 834 142 HOH HOH . J 5 HOH B 35 835 129 HOH HOH . J 5 HOH B 36 836 17 HOH HOH . J 5 HOH B 37 837 82 HOH HOH . J 5 HOH B 38 838 97 HOH HOH . J 5 HOH B 39 839 171 HOH HOH . J 5 HOH B 40 840 47 HOH HOH . J 5 HOH B 41 841 46 HOH HOH . J 5 HOH B 42 842 56 HOH HOH . J 5 HOH B 43 843 128 HOH HOH . J 5 HOH B 44 844 33 HOH HOH . J 5 HOH B 45 845 66 HOH HOH . J 5 HOH B 46 846 146 HOH HOH . J 5 HOH B 47 847 211 HOH HOH . J 5 HOH B 48 848 15 HOH HOH . J 5 HOH B 49 849 10 HOH HOH . J 5 HOH B 50 850 219 HOH HOH . J 5 HOH B 51 851 127 HOH HOH . J 5 HOH B 52 852 50 HOH HOH . J 5 HOH B 53 853 11 HOH HOH . J 5 HOH B 54 854 71 HOH HOH . J 5 HOH B 55 855 109 HOH HOH . J 5 HOH B 56 856 41 HOH HOH . J 5 HOH B 57 857 25 HOH HOH . J 5 HOH B 58 858 156 HOH HOH . J 5 HOH B 59 859 32 HOH HOH . J 5 HOH B 60 860 37 HOH HOH . J 5 HOH B 61 861 188 HOH HOH . J 5 HOH B 62 862 95 HOH HOH . J 5 HOH B 63 863 44 HOH HOH . J 5 HOH B 64 864 7 HOH HOH . J 5 HOH B 65 865 31 HOH HOH . J 5 HOH B 66 866 62 HOH HOH . J 5 HOH B 67 867 174 HOH HOH . J 5 HOH B 68 868 45 HOH HOH . J 5 HOH B 69 869 165 HOH HOH . J 5 HOH B 70 870 89 HOH HOH . J 5 HOH B 71 871 178 HOH HOH . J 5 HOH B 72 872 64 HOH HOH . J 5 HOH B 73 873 94 HOH HOH . J 5 HOH B 74 874 53 HOH HOH . J 5 HOH B 75 875 224 HOH HOH . J 5 HOH B 76 876 18 HOH HOH . J 5 HOH B 77 877 104 HOH HOH . J 5 HOH B 78 878 93 HOH HOH . J 5 HOH B 79 879 214 HOH HOH . J 5 HOH B 80 880 139 HOH HOH . J 5 HOH B 81 881 152 HOH HOH . J 5 HOH B 82 882 222 HOH HOH . J 5 HOH B 83 883 173 HOH HOH . J 5 HOH B 84 884 123 HOH HOH . J 5 HOH B 85 885 208 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 F F1 GTF . . . D 3 -71.173 5.906 -76.974 1 67.18 ? F1 GTF 602 A 1 HETATM 2 N N1 GTF . . . D 3 -71.944 4.17 -75.081 1 56.51 ? N1 GTF 602 A 1 HETATM 3 C C2 GTF . . . D 3 -73.32 3.616 -74.936 1 56.29 ? C2 GTF 602 A 1 HETATM 4 F F2 GTF . . . D 3 -71.896 4.206 -78.254 1 60.85 ? F2 GTF 602 A 1 HETATM 5 O O2 GTF . . . D 3 -73.69 2.771 -75.67 1 57.78 ? O2 GTF 602 A 1 HETATM 6 N N3 GTF . . . D 3 -74.217 4.133 -73.869 1 55.99 ? N3 GTF 602 A 1 HETATM 7 C C4 GTF . . . D 3 -73.758 5.17 -72.97 1 47.56 ? C4 GTF 602 A 1 HETATM 8 N N4 GTF . . . D 3 -74.657 5.673 -71.92 1 57.01 ? N4 GTF 602 A 1 HETATM 9 C C5 GTF . . . D 3 -72.38 5.727 -73.106 1 51.62 ? C5 GTF 602 A 1 HETATM 10 C C6 GTF . . . D 3 -71.471 5.202 -74.173 1 56.33 ? C6 GTF 602 A 1 HETATM 11 P PA GTF . . . D 3 -65.609 3.471 -74.706 1 48.13 ? PA GTF 602 A 1 HETATM 12 P PB GTF . . . D 3 -65.87 6.075 -73.419 1 50.4 ? PB GTF 602 A 1 HETATM 13 P PG GTF . . . D 3 -63.676 5.93 -71.571 1 50.54 ? PG GTF 602 A 1 HETATM 14 C C1' GTF . . . D 3 -71.143 3.678 -76.042 1 59.53 ? C1' GTF 602 A 1 HETATM 15 O O1A GTF . . . D 3 -65.02 2.185 -74.169 1 63.85 ? O1A GTF 602 A 1 HETATM 16 O O1B GTF . . . D 3 -65.055 6.533 -74.602 1 65.3 ? O1B GTF 602 A 1 HETATM 17 O O1G GTF . . . D 3 -62.863 7.043 -70.946 1 54.35 ? O1G GTF 602 A 1 HETATM 18 C C2' GTF . . . D 3 -71.004 4.585 -77.289 1 60.88 ? C2' GTF 602 A 1 HETATM 19 O O2A GTF . . . D 3 -64.622 4.126 -75.659 1 63.56 ? O2A GTF 602 A 1 HETATM 20 O O2B GTF . . . D 3 -67.28 6.633 -73.489 1 59.7 ? O2B GTF 602 A 1 HETATM 21 O O2G GTF . . . D 3 -63.861 4.812 -70.585 1 41.2 ? O2G GTF 602 A 1 HETATM 22 C C3' GTF . . . D 3 -69.811 4.401 -77.704 1 59.38 ? C3' GTF 602 A 1 HETATM 23 O O3' GTF . . . D 3 -69.819 3.669 -78.983 1 67.59 ? O3' GTF 602 A 1 HETATM 24 O O3A GTF . . . D 3 -65.946 4.42 -73.407 1 55.94 ? O3A GTF 602 A 1 HETATM 25 O O3B GTF . . . D 3 -65.148 6.545 -72.005 1 58.7 ? O3B GTF 602 A 1 HETATM 26 O O3G GTF . . . D 3 -62.999 5.399 -72.818 1 64.15 ? O3G GTF 602 A 1 HETATM 27 C C4' GTF . . . D 3 -69.04 3.493 -76.584 1 56.65 ? C4' GTF 602 A 1 HETATM 28 O O4' GTF . . . D 3 -69.705 3.594 -75.517 1 59.27 ? O4' GTF 602 A 1 HETATM 29 C C5' GTF . . . D 3 -67.625 4.012 -76.351 1 57.37 ? C5' GTF 602 A 1 HETATM 30 O O5' GTF . . . D 3 -67.051 3.116 -75.436 1 51.55 ? O5' GTF 602 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #