data_3I3M # _model_server_result.job_id VKowJENo6Humzu7ACMRpdQ _model_server_result.datetime_utc '2024-12-03 14:23:06' _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 3i3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 3I3M # _exptl.entry_id 3I3M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 3 _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 3I3M _cell.length_a 41.444 _cell.length_b 41.444 _cell.length_c 116.709 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I3M _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 B O3' DT 1 B DT 501 1_555 B P ME6 2 B ME6 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale2 B O3' ME6 2 B ME6 502 1_555 B P DT 3 B DT 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? # _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 3I3M _atom_sites.fract_transf_matrix[1][1] 0.024129 _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] 0.024129 _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] 0.008568 _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 AKG A 1 400 400 AKG AKG . D 4 MN A 1 300 300 MN MN . E 5 HOH A 1 601 601 HOH HOH . E 5 HOH A 2 602 602 HOH HOH . E 5 HOH A 3 603 603 HOH HOH . E 5 HOH A 4 604 604 HOH HOH . E 5 HOH A 5 605 605 HOH HOH . E 5 HOH A 6 606 606 HOH HOH . E 5 HOH A 7 607 607 HOH HOH . E 5 HOH A 8 608 608 HOH HOH . E 5 HOH A 9 609 609 HOH HOH . E 5 HOH A 10 610 610 HOH HOH . E 5 HOH A 11 611 611 HOH HOH . E 5 HOH A 12 612 612 HOH HOH . E 5 HOH A 13 613 613 HOH HOH . E 5 HOH A 14 614 614 HOH HOH . E 5 HOH A 15 615 615 HOH HOH . E 5 HOH A 16 616 616 HOH HOH . E 5 HOH A 17 617 617 HOH HOH . E 5 HOH A 18 618 618 HOH HOH . E 5 HOH A 19 619 619 HOH HOH . E 5 HOH A 20 620 620 HOH HOH . E 5 HOH A 21 621 621 HOH HOH . E 5 HOH A 22 622 622 HOH HOH . E 5 HOH A 23 623 623 HOH HOH . E 5 HOH A 24 625 625 HOH HOH . E 5 HOH A 25 626 626 HOH HOH . E 5 HOH A 26 627 627 HOH HOH . E 5 HOH A 27 628 628 HOH HOH . E 5 HOH A 28 629 629 HOH HOH . E 5 HOH A 29 630 630 HOH HOH . E 5 HOH A 30 631 631 HOH HOH . E 5 HOH A 31 632 632 HOH HOH . E 5 HOH A 32 633 633 HOH HOH . E 5 HOH A 33 634 634 HOH HOH . E 5 HOH A 34 635 635 HOH HOH . E 5 HOH A 35 636 636 HOH HOH . E 5 HOH A 36 637 637 HOH HOH . E 5 HOH A 37 638 638 HOH HOH . E 5 HOH A 38 639 639 HOH HOH . E 5 HOH A 39 640 640 HOH HOH . E 5 HOH A 40 641 641 HOH HOH . E 5 HOH A 41 642 642 HOH HOH . E 5 HOH A 42 643 643 HOH HOH . E 5 HOH A 43 644 644 HOH HOH . E 5 HOH A 44 645 645 HOH HOH . E 5 HOH A 45 647 647 HOH HOH . E 5 HOH A 46 648 648 HOH HOH . E 5 HOH A 47 649 649 HOH HOH . E 5 HOH A 48 650 650 HOH HOH . E 5 HOH A 49 651 651 HOH HOH . E 5 HOH A 50 652 652 HOH HOH . E 5 HOH A 51 653 653 HOH HOH . E 5 HOH A 52 654 654 HOH HOH . E 5 HOH A 53 655 655 HOH HOH . E 5 HOH A 54 656 656 HOH HOH . E 5 HOH A 55 658 658 HOH HOH . E 5 HOH A 56 659 659 HOH HOH . E 5 HOH A 57 660 660 HOH HOH . E 5 HOH A 58 661 661 HOH HOH . E 5 HOH A 59 662 662 HOH HOH . E 5 HOH A 60 663 663 HOH HOH . E 5 HOH A 61 664 664 HOH HOH . E 5 HOH A 62 665 665 HOH HOH . E 5 HOH A 63 666 666 HOH HOH . E 5 HOH A 64 667 667 HOH HOH . E 5 HOH A 65 668 668 HOH HOH . E 5 HOH A 66 669 669 HOH HOH . E 5 HOH A 67 670 670 HOH HOH . E 5 HOH A 68 671 671 HOH HOH . E 5 HOH A 69 672 672 HOH HOH . E 5 HOH A 70 673 673 HOH HOH . E 5 HOH A 71 674 674 HOH HOH . E 5 HOH A 72 675 675 HOH HOH . E 5 HOH A 73 676 676 HOH HOH . E 5 HOH A 74 677 677 HOH HOH . E 5 HOH A 75 678 678 HOH HOH . E 5 HOH A 76 679 679 HOH HOH . E 5 HOH A 77 680 680 HOH HOH . E 5 HOH A 78 681 681 HOH HOH . E 5 HOH A 79 683 683 HOH HOH . E 5 HOH A 80 684 684 HOH HOH . E 5 HOH A 81 685 685 HOH HOH . E 5 HOH A 82 686 686 HOH HOH . E 5 HOH A 83 687 687 HOH HOH . E 5 HOH A 84 688 688 HOH HOH . E 5 HOH A 85 689 689 HOH HOH . E 5 HOH A 86 690 690 HOH HOH . E 5 HOH A 87 691 691 HOH HOH . E 5 HOH A 88 692 692 HOH HOH . E 5 HOH A 89 693 693 HOH HOH . E 5 HOH A 90 694 694 HOH HOH . E 5 HOH A 91 695 695 HOH HOH . E 5 HOH A 92 696 696 HOH HOH . E 5 HOH A 93 697 697 HOH HOH . E 5 HOH A 94 698 698 HOH HOH . E 5 HOH A 95 699 699 HOH HOH . E 5 HOH A 96 700 700 HOH HOH . E 5 HOH A 97 701 701 HOH HOH . E 5 HOH A 98 702 702 HOH HOH . E 5 HOH A 99 703 703 HOH HOH . E 5 HOH A 100 704 704 HOH HOH . E 5 HOH A 101 705 705 HOH HOH . E 5 HOH A 102 706 706 HOH HOH . E 5 HOH A 103 708 708 HOH HOH . E 5 HOH A 104 709 709 HOH HOH . E 5 HOH A 105 710 710 HOH HOH . E 5 HOH A 106 711 711 HOH HOH . E 5 HOH A 107 712 712 HOH HOH . E 5 HOH A 108 713 713 HOH HOH . E 5 HOH A 109 714 714 HOH HOH . E 5 HOH A 110 716 716 HOH HOH . E 5 HOH A 111 717 717 HOH HOH . E 5 HOH A 112 718 718 HOH HOH . E 5 HOH A 113 719 719 HOH HOH . E 5 HOH A 114 720 720 HOH HOH . E 5 HOH A 115 721 721 HOH HOH . E 5 HOH A 116 722 722 HOH HOH . E 5 HOH A 117 723 723 HOH HOH . E 5 HOH A 118 724 724 HOH HOH . E 5 HOH A 119 725 725 HOH HOH . E 5 HOH A 120 726 726 HOH HOH . E 5 HOH A 121 727 727 HOH HOH . E 5 HOH A 122 728 728 HOH HOH . E 5 HOH A 123 729 729 HOH HOH . E 5 HOH A 124 730 730 HOH HOH . E 5 HOH A 125 731 731 HOH HOH . E 5 HOH A 126 732 732 HOH HOH . E 5 HOH A 127 733 733 HOH HOH . E 5 HOH A 128 734 734 HOH HOH . E 5 HOH A 129 735 735 HOH HOH . E 5 HOH A 130 736 736 HOH HOH . E 5 HOH A 131 738 738 HOH HOH . E 5 HOH A 132 739 739 HOH HOH . E 5 HOH A 133 740 740 HOH HOH . E 5 HOH A 134 741 741 HOH HOH . E 5 HOH A 135 742 742 HOH HOH . E 5 HOH A 136 743 743 HOH HOH . E 5 HOH A 137 744 744 HOH HOH . E 5 HOH A 138 745 745 HOH HOH . E 5 HOH A 139 746 746 HOH HOH . E 5 HOH A 140 747 747 HOH HOH . E 5 HOH A 141 748 748 HOH HOH . F 5 HOH B 1 624 624 HOH HOH . F 5 HOH B 2 646 646 HOH HOH . F 5 HOH B 3 657 657 HOH HOH . F 5 HOH B 4 682 682 HOH HOH . F 5 HOH B 5 707 707 HOH HOH . F 5 HOH B 6 715 715 HOH HOH . F 5 HOH B 7 737 737 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 . . . C 3 5.457 16.66 2.962 1 12.28 ? C1 AKG 400 A 1 HETATM 2 O O1 AKG . . . C 3 6.246 15.998 2.312 1 13.4 ? O1 AKG 400 A 1 HETATM 3 O O2 AKG . . . C 3 5.821 17.871 3.412 1 12.82 ? O2 AKG 400 A 1 HETATM 4 C C2 AKG . . . C 3 4.024 16.245 3.063 1 11.74 ? C2 AKG 400 A 1 HETATM 5 O O5 AKG . . . C 3 3.226 16.998 3.586 1 9.58 ? O5 AKG 400 A 1 HETATM 6 C C3 AKG . . . C 3 3.585 14.886 2.552 1 9.46 ? C3 AKG 400 A 1 HETATM 7 C C4 AKG . . . C 3 2.055 14.809 2.431 1 11.31 ? C4 AKG 400 A 1 HETATM 8 C C5 AKG . . . C 3 1.63 13.512 1.783 1 9.56 ? C5 AKG 400 A 1 HETATM 9 O O3 AKG . . . C 3 2.202 12.479 2.038 1 8.73 ? O3 AKG 400 A 1 HETATM 10 O O4 AKG . . . C 3 0.513 13.482 1.058 1 10.53 ? O4 AKG 400 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #