data_2FDF # _model_server_result.job_id yWQsaM5tr8hOOucSmMla0g _model_server_result.datetime_utc '2024-12-11 07:34:20' _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 2fdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 2FDF # _exptl.entry_id 2FDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC ACID' _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 90 _cell.entry_id 2FDF _cell.length_a 41.294 _cell.length_b 41.294 _cell.length_c 116.797 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 A O3' DT 1 B DT 501 1_555 A P MA7 2 B MA7 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale2 A O3' MA7 2 B MA7 502 1_555 A P DT 3 B DT 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 B NE2 HIS 121 A HIS 131 1_555 C CO CO . A CO 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc2 B OD1 ASP 123 A ASP 133 1_555 C CO CO . A CO 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 B NE2 HIS 177 A HIS 187 1_555 C CO CO . A CO 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc4 C CO CO . A CO 300 1_555 D O2 AKG . A AKG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 C CO CO . A CO 300 1_555 D O5 AKG . A AKG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 C CO CO . A CO 300 1_555 F O HOH . A HOH 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? # _chem_comp.formula 'C5 H6 O5' _chem_comp.formula_weight 146.098 _chem_comp.id AKG _chem_comp.mon_nstd_flag . _chem_comp.name '2-OXOGLUTARIC ACID' _chem_comp.type non-polymer _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 C1 O1 AKG doub 1 n n C1 O2 AKG sing 2 n n C1 C2 AKG sing 3 n n O2 HO2 AKG sing 4 n n C2 O5 AKG doub 5 n n C2 C3 AKG sing 6 n n C3 C4 AKG sing 7 n n C3 H31 AKG sing 8 n n C3 H32 AKG sing 9 n n C4 C5 AKG sing 10 n n C4 H41 AKG sing 11 n n C4 H42 AKG sing 12 n n C5 O3 AKG doub 13 n n C5 O4 AKG sing 14 n n O4 HO4 AKG sing 15 n n # _atom_sites.entry_id 2FDF _atom_sites.fract_transf_matrix[1][1] 0.024217 _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] 0.024217 _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] 0.008562 _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 CO A 1 300 300 CO CO . D 4 AKG A 1 400 400 AKG AKG . E 5 HOH B 1 602 602 HOH HOH . E 5 HOH B 2 603 603 HOH HOH . E 5 HOH B 3 622 622 HOH HOH . E 5 HOH B 4 638 638 HOH HOH . E 5 HOH B 5 640 640 HOH HOH . E 5 HOH B 6 656 656 HOH HOH . E 5 HOH B 7 663 663 HOH HOH . E 5 HOH B 8 699 699 HOH HOH . E 5 HOH B 9 701 701 HOH HOH . E 5 HOH B 10 721 721 HOH HOH . E 5 HOH B 11 723 723 HOH HOH . E 5 HOH B 12 742 742 HOH HOH . E 5 HOH B 13 799 799 HOH HOH . E 5 HOH B 14 825 825 HOH HOH . F 5 HOH A 1 601 601 HOH HOH . F 5 HOH A 2 604 604 HOH HOH . F 5 HOH A 3 605 605 HOH HOH . F 5 HOH A 4 606 606 HOH HOH . F 5 HOH A 5 607 607 HOH HOH . F 5 HOH A 6 608 608 HOH HOH . F 5 HOH A 7 609 609 HOH HOH . F 5 HOH A 8 610 610 HOH HOH . F 5 HOH A 9 611 611 HOH HOH . F 5 HOH A 10 612 612 HOH HOH . F 5 HOH A 11 613 613 HOH HOH . F 5 HOH A 12 614 614 HOH HOH . F 5 HOH A 13 615 615 HOH HOH . F 5 HOH A 14 616 616 HOH HOH . F 5 HOH A 15 617 617 HOH HOH . F 5 HOH A 16 618 618 HOH HOH . F 5 HOH A 17 619 619 HOH HOH . F 5 HOH A 18 620 620 HOH HOH . F 5 HOH A 19 621 621 HOH HOH . F 5 HOH A 20 623 623 HOH HOH . F 5 HOH A 21 624 624 HOH HOH . F 5 HOH A 22 625 625 HOH HOH . F 5 HOH A 23 626 626 HOH HOH . F 5 HOH A 24 627 627 HOH HOH . F 5 HOH A 25 628 628 HOH HOH . F 5 HOH A 26 629 629 HOH HOH . F 5 HOH A 27 630 630 HOH HOH . F 5 HOH A 28 631 631 HOH HOH . F 5 HOH A 29 632 632 HOH HOH . F 5 HOH A 30 633 633 HOH HOH . F 5 HOH A 31 634 634 HOH HOH . F 5 HOH A 32 635 635 HOH HOH . F 5 HOH A 33 636 636 HOH HOH . F 5 HOH A 34 637 637 HOH HOH . F 5 HOH A 35 639 639 HOH HOH . F 5 HOH A 36 641 641 HOH HOH . F 5 HOH A 37 642 642 HOH HOH . F 5 HOH A 38 643 643 HOH HOH . F 5 HOH A 39 644 644 HOH HOH . F 5 HOH A 40 645 645 HOH HOH . F 5 HOH A 41 646 646 HOH HOH . F 5 HOH A 42 647 647 HOH HOH . F 5 HOH A 43 648 648 HOH HOH . F 5 HOH A 44 649 649 HOH HOH . F 5 HOH A 45 650 650 HOH HOH . F 5 HOH A 46 651 651 HOH HOH . F 5 HOH A 47 652 652 HOH HOH . F 5 HOH A 48 653 653 HOH HOH . F 5 HOH A 49 654 654 HOH HOH . F 5 HOH A 50 655 655 HOH HOH . F 5 HOH A 51 657 657 HOH HOH . F 5 HOH A 52 658 658 HOH HOH . F 5 HOH A 53 659 659 HOH HOH . F 5 HOH A 54 660 660 HOH HOH . F 5 HOH A 55 661 661 HOH HOH . F 5 HOH A 56 662 662 HOH HOH . F 5 HOH A 57 664 664 HOH HOH . F 5 HOH A 58 665 665 HOH HOH . F 5 HOH A 59 666 666 HOH HOH . F 5 HOH A 60 667 667 HOH HOH . F 5 HOH A 61 668 668 HOH HOH . F 5 HOH A 62 669 669 HOH HOH . F 5 HOH A 63 670 670 HOH HOH . F 5 HOH A 64 671 671 HOH HOH . F 5 HOH A 65 672 672 HOH HOH . F 5 HOH A 66 673 673 HOH HOH . F 5 HOH A 67 674 674 HOH HOH . F 5 HOH A 68 675 675 HOH HOH . F 5 HOH A 69 676 676 HOH HOH . F 5 HOH A 70 677 677 HOH HOH . F 5 HOH A 71 678 678 HOH HOH . F 5 HOH A 72 679 679 HOH HOH . F 5 HOH A 73 680 680 HOH HOH . F 5 HOH A 74 681 681 HOH HOH . F 5 HOH A 75 682 682 HOH HOH . F 5 HOH A 76 683 683 HOH HOH . F 5 HOH A 77 684 684 HOH HOH . F 5 HOH A 78 685 685 HOH HOH . F 5 HOH A 79 686 686 HOH HOH . F 5 HOH A 80 687 687 HOH HOH . F 5 HOH A 81 688 688 HOH HOH . F 5 HOH A 82 689 689 HOH HOH . F 5 HOH A 83 690 690 HOH HOH . F 5 HOH A 84 691 691 HOH HOH . F 5 HOH A 85 692 692 HOH HOH . F 5 HOH A 86 693 693 HOH HOH . F 5 HOH A 87 694 694 HOH HOH . F 5 HOH A 88 695 695 HOH HOH . F 5 HOH A 89 696 696 HOH HOH . F 5 HOH A 90 697 697 HOH HOH . F 5 HOH A 91 698 698 HOH HOH . F 5 HOH A 92 700 700 HOH HOH . F 5 HOH A 93 702 702 HOH HOH . F 5 HOH A 94 703 703 HOH HOH . F 5 HOH A 95 704 704 HOH HOH . F 5 HOH A 96 705 705 HOH HOH . F 5 HOH A 97 706 706 HOH HOH . F 5 HOH A 98 707 707 HOH HOH . F 5 HOH A 99 708 708 HOH HOH . F 5 HOH A 100 709 709 HOH HOH . F 5 HOH A 101 710 710 HOH HOH . F 5 HOH A 102 711 711 HOH HOH . F 5 HOH A 103 712 712 HOH HOH . F 5 HOH A 104 713 713 HOH HOH . F 5 HOH A 105 714 714 HOH HOH . F 5 HOH A 106 715 715 HOH HOH . F 5 HOH A 107 716 716 HOH HOH . F 5 HOH A 108 717 717 HOH HOH . F 5 HOH A 109 718 718 HOH HOH . F 5 HOH A 110 719 719 HOH HOH . F 5 HOH A 111 720 720 HOH HOH . F 5 HOH A 112 722 722 HOH HOH . F 5 HOH A 113 724 724 HOH HOH . F 5 HOH A 114 725 725 HOH HOH . F 5 HOH A 115 726 726 HOH HOH . F 5 HOH A 116 727 727 HOH HOH . F 5 HOH A 117 728 728 HOH HOH . F 5 HOH A 118 729 729 HOH HOH . F 5 HOH A 119 730 730 HOH HOH . F 5 HOH A 120 731 731 HOH HOH . F 5 HOH A 121 732 732 HOH HOH . F 5 HOH A 122 733 733 HOH HOH . F 5 HOH A 123 734 734 HOH HOH . F 5 HOH A 124 735 735 HOH HOH . F 5 HOH A 125 736 736 HOH HOH . F 5 HOH A 126 737 737 HOH HOH . F 5 HOH A 127 738 738 HOH HOH . F 5 HOH A 128 739 739 HOH HOH . F 5 HOH A 129 740 740 HOH HOH . F 5 HOH A 130 741 741 HOH HOH . F 5 HOH A 131 743 743 HOH HOH . F 5 HOH A 132 744 744 HOH HOH . F 5 HOH A 133 745 745 HOH HOH . F 5 HOH A 134 746 746 HOH HOH . F 5 HOH A 135 747 747 HOH HOH . F 5 HOH A 136 748 748 HOH HOH . F 5 HOH A 137 749 749 HOH HOH . F 5 HOH A 138 750 750 HOH HOH . F 5 HOH A 139 751 751 HOH HOH . F 5 HOH A 140 752 752 HOH HOH . F 5 HOH A 141 753 753 HOH HOH . F 5 HOH A 142 754 754 HOH HOH . F 5 HOH A 143 755 755 HOH HOH . F 5 HOH A 144 756 756 HOH HOH . F 5 HOH A 145 757 757 HOH HOH . F 5 HOH A 146 758 758 HOH HOH . F 5 HOH A 147 759 759 HOH HOH . F 5 HOH A 148 760 760 HOH HOH . F 5 HOH A 149 761 761 HOH HOH . F 5 HOH A 150 762 762 HOH HOH . F 5 HOH A 151 763 763 HOH HOH . F 5 HOH A 152 764 764 HOH HOH . F 5 HOH A 153 765 765 HOH HOH . F 5 HOH A 154 766 766 HOH HOH . F 5 HOH A 155 767 767 HOH HOH . F 5 HOH A 156 768 768 HOH HOH . F 5 HOH A 157 769 769 HOH HOH . F 5 HOH A 158 770 770 HOH HOH . F 5 HOH A 159 771 771 HOH HOH . F 5 HOH A 160 772 772 HOH HOH . F 5 HOH A 161 773 773 HOH HOH . F 5 HOH A 162 774 774 HOH HOH . F 5 HOH A 163 775 775 HOH HOH . F 5 HOH A 164 776 776 HOH HOH . F 5 HOH A 165 777 777 HOH HOH . F 5 HOH A 166 778 778 HOH HOH . F 5 HOH A 167 779 779 HOH HOH . F 5 HOH A 168 780 780 HOH HOH . F 5 HOH A 169 781 781 HOH HOH . F 5 HOH A 170 782 782 HOH HOH . F 5 HOH A 171 783 783 HOH HOH . F 5 HOH A 172 784 784 HOH HOH . F 5 HOH A 173 785 785 HOH HOH . F 5 HOH A 174 786 786 HOH HOH . F 5 HOH A 175 787 787 HOH HOH . F 5 HOH A 176 788 788 HOH HOH . F 5 HOH A 177 789 789 HOH HOH . F 5 HOH A 178 790 790 HOH HOH . F 5 HOH A 179 791 791 HOH HOH . F 5 HOH A 180 792 792 HOH HOH . F 5 HOH A 181 793 793 HOH HOH . F 5 HOH A 182 794 794 HOH HOH . F 5 HOH A 183 795 795 HOH HOH . F 5 HOH A 184 796 796 HOH HOH . F 5 HOH A 185 797 797 HOH HOH . F 5 HOH A 186 798 798 HOH HOH . F 5 HOH A 187 800 800 HOH HOH . F 5 HOH A 188 801 801 HOH HOH . F 5 HOH A 189 802 802 HOH HOH . F 5 HOH A 190 803 803 HOH HOH . F 5 HOH A 191 804 804 HOH HOH . F 5 HOH A 192 805 805 HOH HOH . F 5 HOH A 193 806 806 HOH HOH . F 5 HOH A 194 807 807 HOH HOH . F 5 HOH A 195 808 808 HOH HOH . F 5 HOH A 196 809 809 HOH HOH . F 5 HOH A 197 810 810 HOH HOH . F 5 HOH A 198 811 811 HOH HOH . F 5 HOH A 199 812 812 HOH HOH . F 5 HOH A 200 813 813 HOH HOH . F 5 HOH A 201 814 814 HOH HOH . F 5 HOH A 202 815 815 HOH HOH . F 5 HOH A 203 816 816 HOH HOH . F 5 HOH A 204 817 817 HOH HOH . F 5 HOH A 205 818 818 HOH HOH . F 5 HOH A 206 819 819 HOH HOH . F 5 HOH A 207 820 820 HOH HOH . F 5 HOH A 208 821 821 HOH HOH . F 5 HOH A 209 822 822 HOH HOH . F 5 HOH A 210 823 823 HOH HOH . F 5 HOH A 211 824 824 HOH HOH . F 5 HOH A 212 826 826 HOH HOH . F 5 HOH A 213 827 827 HOH HOH . F 5 HOH A 214 828 828 HOH HOH . F 5 HOH A 215 829 829 HOH HOH . F 5 HOH A 216 830 830 HOH HOH . F 5 HOH A 217 831 831 HOH HOH . F 5 HOH A 218 832 832 HOH HOH . F 5 HOH A 219 833 833 HOH HOH . F 5 HOH A 220 834 834 HOH HOH . F 5 HOH A 221 835 835 HOH HOH . F 5 HOH A 222 836 836 HOH HOH . F 5 HOH A 223 837 837 HOH HOH . F 5 HOH A 224 838 838 HOH HOH . F 5 HOH A 225 839 839 HOH HOH . F 5 HOH A 226 840 840 HOH HOH . F 5 HOH A 227 841 841 HOH HOH . F 5 HOH A 228 842 842 HOH HOH . F 5 HOH A 229 843 843 HOH HOH . F 5 HOH A 230 844 844 HOH HOH . F 5 HOH A 231 845 845 HOH HOH . F 5 HOH A 232 846 846 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 C C1 AKG . . . D 4 26.188 37.12 57.332 1 10.36 ? C1 AKG 400 A 1 HETATM 2 O O1 AKG . . . D 4 27.005 36.372 56.838 1 12.35 ? O1 AKG 400 A 1 HETATM 3 O O2 AKG . . . D 4 26.568 38.31 57.802 1 5.87 ? O2 AKG 400 A 1 HETATM 4 C C2 AKG . . . D 4 24.742 36.793 57.288 1 9.41 ? C2 AKG 400 A 1 HETATM 5 O O5 AKG . . . D 4 23.961 37.543 57.821 1 10.32 ? O5 AKG 400 A 1 HETATM 6 C C3 AKG . . . D 4 24.273 35.495 56.671 1 9.32 ? C3 AKG 400 A 1 HETATM 7 C C4 AKG . . . D 4 22.745 35.485 56.508 1 11.22 ? C4 AKG 400 A 1 HETATM 8 C C5 AKG . . . D 4 22.281 34.128 56.05 1 11.24 ? C5 AKG 400 A 1 HETATM 9 O O3 AKG . . . D 4 22.913 33.139 56.327 1 13.37 ? O3 AKG 400 A 1 HETATM 10 O O4 AKG . . . D 4 21.244 34.023 55.219 1 12.27 ? O4 AKG 400 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #