data_2FDK # _model_server_result.job_id WCZaFmbOMXNQghmDqLGk4g _model_server_result.datetime_utc '2024-11-22 11:21:23' _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 2fdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 2FDK # _exptl.entry_id 2FDK _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 2FDK _cell.length_a 40.576 _cell.length_b 40.576 _cell.length_c 117.049 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FDK _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,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 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale2 A O3' MA7 2 B MA7 502 1_555 A P DT 3 B DT 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? metalc ? metalc1 B NE2 HIS 121 A HIS 131 1_555 C FE FE2 . A FE2 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc2 B OD1 ASP 123 A ASP 133 1_555 C FE FE2 . A FE2 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc3 B NE2 HIS 177 A HIS 187 1_555 C FE FE2 . A FE2 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc4 C FE FE2 . A FE2 300 1_555 D O2 AKG . A AKG 400 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.117 ? metalc ? metalc5 C FE FE2 . A FE2 300 1_555 D O5 AKG . A AKG 400 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.361 ? metalc ? metalc6 C FE FE2 . A FE2 300 1_555 E O1 SIN . A SIN 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.264 ? metalc ? metalc7 C FE FE2 . A FE2 300 1_555 G O HOH . A HOH 720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc8 C FE FE2 . A FE2 300 1_555 G O HOH . A HOH 792 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.456 ? # _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 2FDK _atom_sites.fract_transf_matrix[1][1] 0.024645 _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] 0.024645 _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] 0.008543 _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 FE2 A 1 300 300 FE2 FE2 . D 4 AKG A 1 400 400 AKG AKG . E 5 SIN A 1 401 401 SIN SIN . F 6 HOH B 1 602 602 HOH HOH . F 6 HOH B 2 607 607 HOH HOH . F 6 HOH B 3 629 629 HOH HOH . F 6 HOH B 4 634 634 HOH HOH . F 6 HOH B 5 635 635 HOH HOH . F 6 HOH B 6 690 690 HOH HOH . F 6 HOH B 7 712 712 HOH HOH . F 6 HOH B 8 715 715 HOH HOH . F 6 HOH B 9 717 717 HOH HOH . F 6 HOH B 10 725 725 HOH HOH . F 6 HOH B 11 735 735 HOH HOH . F 6 HOH B 12 748 748 HOH HOH . F 6 HOH B 13 753 753 HOH HOH . F 6 HOH B 14 765 765 HOH HOH . F 6 HOH B 15 776 776 HOH HOH . G 6 HOH A 1 601 601 HOH HOH . G 6 HOH A 2 603 603 HOH HOH . G 6 HOH A 3 604 604 HOH HOH . G 6 HOH A 4 605 605 HOH HOH . G 6 HOH A 5 606 606 HOH HOH . G 6 HOH A 6 608 608 HOH HOH . G 6 HOH A 7 609 609 HOH HOH . G 6 HOH A 8 610 610 HOH HOH . G 6 HOH A 9 611 611 HOH HOH . G 6 HOH A 10 612 612 HOH HOH . G 6 HOH A 11 613 613 HOH HOH . G 6 HOH A 12 614 614 HOH HOH . G 6 HOH A 13 615 615 HOH HOH . G 6 HOH A 14 616 616 HOH HOH . G 6 HOH A 15 617 617 HOH HOH . G 6 HOH A 16 618 618 HOH HOH . G 6 HOH A 17 619 619 HOH HOH . G 6 HOH A 18 620 620 HOH HOH . G 6 HOH A 19 621 621 HOH HOH . G 6 HOH A 20 622 622 HOH HOH . G 6 HOH A 21 623 623 HOH HOH . G 6 HOH A 22 624 624 HOH HOH . G 6 HOH A 23 625 625 HOH HOH . G 6 HOH A 24 626 626 HOH HOH . G 6 HOH A 25 627 627 HOH HOH . G 6 HOH A 26 628 628 HOH HOH . G 6 HOH A 27 630 630 HOH HOH . G 6 HOH A 28 631 631 HOH HOH . G 6 HOH A 29 632 632 HOH HOH . G 6 HOH A 30 633 633 HOH HOH . G 6 HOH A 31 636 636 HOH HOH . G 6 HOH A 32 637 637 HOH HOH . G 6 HOH A 33 638 638 HOH HOH . G 6 HOH A 34 639 639 HOH HOH . G 6 HOH A 35 640 640 HOH HOH . G 6 HOH A 36 641 641 HOH HOH . G 6 HOH A 37 642 642 HOH HOH . G 6 HOH A 38 643 643 HOH HOH . G 6 HOH A 39 644 644 HOH HOH . G 6 HOH A 40 645 645 HOH HOH . G 6 HOH A 41 646 646 HOH HOH . G 6 HOH A 42 647 647 HOH HOH . G 6 HOH A 43 648 648 HOH HOH . G 6 HOH A 44 649 649 HOH HOH . G 6 HOH A 45 650 650 HOH HOH . G 6 HOH A 46 651 651 HOH HOH . G 6 HOH A 47 652 652 HOH HOH . G 6 HOH A 48 653 653 HOH HOH . G 6 HOH A 49 654 654 HOH HOH . G 6 HOH A 50 655 655 HOH HOH . G 6 HOH A 51 656 656 HOH HOH . G 6 HOH A 52 657 657 HOH HOH . G 6 HOH A 53 658 658 HOH HOH . G 6 HOH A 54 659 659 HOH HOH . G 6 HOH A 55 660 660 HOH HOH . G 6 HOH A 56 661 661 HOH HOH . G 6 HOH A 57 662 662 HOH HOH . G 6 HOH A 58 663 663 HOH HOH . G 6 HOH A 59 664 664 HOH HOH . G 6 HOH A 60 665 665 HOH HOH . G 6 HOH A 61 666 666 HOH HOH . G 6 HOH A 62 667 667 HOH HOH . G 6 HOH A 63 668 668 HOH HOH . G 6 HOH A 64 669 669 HOH HOH . G 6 HOH A 65 670 670 HOH HOH . G 6 HOH A 66 671 671 HOH HOH . G 6 HOH A 67 672 672 HOH HOH . G 6 HOH A 68 673 673 HOH HOH . G 6 HOH A 69 674 674 HOH HOH . G 6 HOH A 70 675 675 HOH HOH . G 6 HOH A 71 676 676 HOH HOH . G 6 HOH A 72 677 677 HOH HOH . G 6 HOH A 73 678 678 HOH HOH . G 6 HOH A 74 679 679 HOH HOH . G 6 HOH A 75 680 680 HOH HOH . G 6 HOH A 76 681 681 HOH HOH . G 6 HOH A 77 682 682 HOH HOH . G 6 HOH A 78 683 683 HOH HOH . G 6 HOH A 79 684 684 HOH HOH . G 6 HOH A 80 685 685 HOH HOH . G 6 HOH A 81 686 686 HOH HOH . G 6 HOH A 82 687 687 HOH HOH . G 6 HOH A 83 688 688 HOH HOH . G 6 HOH A 84 689 689 HOH HOH . G 6 HOH A 85 691 691 HOH HOH . G 6 HOH A 86 692 692 HOH HOH . G 6 HOH A 87 693 693 HOH HOH . G 6 HOH A 88 694 694 HOH HOH . G 6 HOH A 89 695 695 HOH HOH . G 6 HOH A 90 696 696 HOH HOH . G 6 HOH A 91 697 697 HOH HOH . G 6 HOH A 92 698 698 HOH HOH . G 6 HOH A 93 699 699 HOH HOH . G 6 HOH A 94 700 700 HOH HOH . G 6 HOH A 95 701 701 HOH HOH . G 6 HOH A 96 702 702 HOH HOH . G 6 HOH A 97 703 703 HOH HOH . G 6 HOH A 98 704 704 HOH HOH . G 6 HOH A 99 705 705 HOH HOH . G 6 HOH A 100 706 706 HOH HOH . G 6 HOH A 101 707 707 HOH HOH . G 6 HOH A 102 708 708 HOH HOH . G 6 HOH A 103 709 709 HOH HOH . G 6 HOH A 104 710 710 HOH HOH . G 6 HOH A 105 711 711 HOH HOH . G 6 HOH A 106 713 713 HOH HOH . G 6 HOH A 107 714 714 HOH HOH . G 6 HOH A 108 716 716 HOH HOH . G 6 HOH A 109 718 718 HOH HOH . G 6 HOH A 110 719 719 HOH HOH . G 6 HOH A 111 720 720 HOH HOH . G 6 HOH A 112 721 721 HOH HOH . G 6 HOH A 113 722 722 HOH HOH . G 6 HOH A 114 723 723 HOH HOH . G 6 HOH A 115 724 724 HOH HOH . G 6 HOH A 116 726 726 HOH HOH . G 6 HOH A 117 727 727 HOH HOH . G 6 HOH A 118 728 728 HOH HOH . G 6 HOH A 119 729 729 HOH HOH . G 6 HOH A 120 730 730 HOH HOH . G 6 HOH A 121 731 731 HOH HOH . G 6 HOH A 122 732 732 HOH HOH . G 6 HOH A 123 733 733 HOH HOH . G 6 HOH A 124 734 734 HOH HOH . G 6 HOH A 125 736 736 HOH HOH . G 6 HOH A 126 737 737 HOH HOH . G 6 HOH A 127 738 738 HOH HOH . G 6 HOH A 128 739 739 HOH HOH . G 6 HOH A 129 740 740 HOH HOH . G 6 HOH A 130 741 741 HOH HOH . G 6 HOH A 131 742 742 HOH HOH . G 6 HOH A 132 743 743 HOH HOH . G 6 HOH A 133 744 744 HOH HOH . G 6 HOH A 134 745 745 HOH HOH . G 6 HOH A 135 746 746 HOH HOH . G 6 HOH A 136 747 747 HOH HOH . G 6 HOH A 137 749 749 HOH HOH . G 6 HOH A 138 750 750 HOH HOH . G 6 HOH A 139 751 751 HOH HOH . G 6 HOH A 140 752 752 HOH HOH . G 6 HOH A 141 754 754 HOH HOH . G 6 HOH A 142 755 755 HOH HOH . G 6 HOH A 143 756 756 HOH HOH . G 6 HOH A 144 757 757 HOH HOH . G 6 HOH A 145 758 758 HOH HOH . G 6 HOH A 146 759 759 HOH HOH . G 6 HOH A 147 760 760 HOH HOH . G 6 HOH A 148 761 761 HOH HOH . G 6 HOH A 149 762 762 HOH HOH . G 6 HOH A 150 763 763 HOH HOH . G 6 HOH A 151 764 764 HOH HOH . G 6 HOH A 152 766 766 HOH HOH . G 6 HOH A 153 767 767 HOH HOH . G 6 HOH A 154 768 768 HOH HOH . G 6 HOH A 155 769 769 HOH HOH . G 6 HOH A 156 770 770 HOH HOH . G 6 HOH A 157 771 771 HOH HOH . G 6 HOH A 158 772 772 HOH HOH . G 6 HOH A 159 773 773 HOH HOH . G 6 HOH A 160 774 774 HOH HOH . G 6 HOH A 161 775 775 HOH HOH . G 6 HOH A 162 777 777 HOH HOH . G 6 HOH A 163 778 778 HOH HOH . G 6 HOH A 164 779 779 HOH HOH . G 6 HOH A 165 780 780 HOH HOH . G 6 HOH A 166 781 781 HOH HOH . G 6 HOH A 167 782 782 HOH HOH . G 6 HOH A 168 783 783 HOH HOH . G 6 HOH A 169 784 784 HOH HOH . G 6 HOH A 170 785 785 HOH HOH . G 6 HOH A 171 786 786 HOH HOH . G 6 HOH A 172 787 787 HOH HOH . G 6 HOH A 173 788 788 HOH HOH . G 6 HOH A 174 789 789 HOH HOH . G 6 HOH A 175 790 790 HOH HOH . G 6 HOH A 176 791 791 HOH HOH . G 6 HOH A 177 792 792 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 . A . D 4 16.609 4.571 -4.153 0.07 37.16 ? C1 AKG 400 A 1 HETATM 2 O O1 AKG . A . D 4 15.701 5.31 -4.49 0.07 37.21 ? O1 AKG 400 A 1 HETATM 3 O O2 AKG . A . D 4 17.872 5.004 -4.197 0.07 37.08 ? O2 AKG 400 A 1 HETATM 4 C C2 AKG . A . D 4 16.325 3.149 -3.805 0.07 37.17 ? C2 AKG 400 A 1 HETATM 5 O O5 AKG . A . D 4 17.209 2.324 -3.892 0.07 37.25 ? O5 AKG 400 A 1 HETATM 6 C C3 AKG . A . D 4 14.964 2.762 -3.257 0.07 37.1 ? C3 AKG 400 A 1 HETATM 7 C C4 AKG . A . D 4 14.524 1.413 -3.832 0.07 36.91 ? C4 AKG 400 A 1 HETATM 8 C C5 AKG . A . D 4 13.367 0.86 -3.036 0.07 36.8 ? C5 AKG 400 A 1 HETATM 9 O O3 AKG . A . D 4 12.338 1.491 -2.938 0.07 36.68 ? O3 AKG 400 A 1 HETATM 10 O O4 AKG . A . D 4 13.53 -0.268 -2.335 0.07 36.73 ? O4 AKG 400 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #