data_5YFN # _model_server_result.job_id KNpcz--Atb9e1oXOlrufKw _model_server_result.datetime_utc '2024-10-10 07:19:34' _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 5yfn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5YFN # _exptl.entry_id 5YFN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ISOCITRIC ACID' _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 109.94 _cell.angle_gamma 90 _cell.entry_id 5YFN _cell.length_a 111.56 _cell.length_b 92 _cell.length_c 138.835 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YFN _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # _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,G,H,I,J _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 # 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 G 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 A OD2 ASP 259 A ASP 252 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc2 A OD1 ASP 282 A ASP 275 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 C MG MG . A MG 501 1_555 D O2 ICT . A ICT 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc4 C MG MG . A MG 501 1_555 D O7 ICT . A ICT 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc5 C MG MG . A MG 501 1_555 B OD2 ASP 259 B ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc6 E MG MG . A MG 503 1_555 G O1 ICT . A ICT 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc7 E MG MG . A MG 503 1_555 G O7 ICT . A ICT 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc8 E MG MG . A MG 503 1_555 B OD1 ASP 282 B ASP 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _chem_comp.formula 'C6 H8 O7' _chem_comp.formula_weight 192.124 _chem_comp.id ICT _chem_comp.mon_nstd_flag . _chem_comp.name 'ISOCITRIC 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 ICT doub 152 n n C1 O2 ICT sing 153 n n C1 C2 ICT sing 154 n n O2 HO2 ICT sing 155 n n C2 O7 ICT sing 156 n n C2 C3 ICT sing 157 n n C2 H2 ICT sing 158 n n O7 HO7 ICT sing 159 n n C3 C4 ICT sing 160 n n C3 C6 ICT sing 161 n n C3 H3 ICT sing 162 n n C4 C5 ICT sing 163 n n C4 H41 ICT sing 164 n n C4 H42 ICT sing 165 n n C5 O3 ICT doub 166 n n C5 O4 ICT sing 167 n n O4 HO4 ICT sing 168 n n C6 O5 ICT doub 169 n n C6 O6 ICT sing 170 n n O6 HO6 ICT sing 171 n n # _atom_sites.entry_id 5YFN _atom_sites.fract_transf_matrix[1][1] 0.008964 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003251 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01087 _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] 0.007662 _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 MG A 1 501 501 MG MG . D 3 ICT A 1 502 503 ICT ICT . E 2 MG A 1 503 501 MG MG . F 4 K A 1 504 502 K K . G 3 ICT A 1 505 503 ICT ICT . H 4 K B 1 501 502 K K . I 5 HOH A 1 601 601 HOH HOH . I 5 HOH A 2 602 609 HOH HOH . I 5 HOH A 3 603 602 HOH HOH . I 5 HOH A 4 604 603 HOH HOH . I 5 HOH A 5 605 604 HOH HOH . I 5 HOH A 6 606 605 HOH HOH . I 5 HOH A 7 607 606 HOH HOH . I 5 HOH A 8 608 607 HOH HOH . I 5 HOH A 9 609 608 HOH HOH . I 5 HOH A 10 610 610 HOH HOH . I 5 HOH A 11 611 611 HOH HOH . I 5 HOH A 12 612 613 HOH HOH . I 5 HOH A 13 613 614 HOH HOH . I 5 HOH A 14 614 612 HOH HOH . I 5 HOH A 15 615 615 HOH HOH . I 5 HOH A 16 616 616 HOH HOH . I 5 HOH A 17 617 617 HOH HOH . I 5 HOH A 18 618 618 HOH HOH . I 5 HOH A 19 619 619 HOH HOH . I 5 HOH A 20 620 620 HOH HOH . I 5 HOH A 21 621 621 HOH HOH . I 5 HOH A 22 622 622 HOH HOH . I 5 HOH A 23 623 623 HOH HOH . I 5 HOH A 24 624 624 HOH HOH . I 5 HOH A 25 625 625 HOH HOH . I 5 HOH A 26 626 626 HOH HOH . I 5 HOH A 27 627 627 HOH HOH . I 5 HOH A 28 628 628 HOH HOH . I 5 HOH A 29 629 629 HOH HOH . I 5 HOH A 30 630 630 HOH HOH . I 5 HOH A 31 631 631 HOH HOH . I 5 HOH A 32 632 632 HOH HOH . I 5 HOH A 33 633 633 HOH HOH . I 5 HOH A 34 634 634 HOH HOH . I 5 HOH A 35 635 635 HOH HOH . I 5 HOH A 36 636 636 HOH HOH . I 5 HOH A 37 637 637 HOH HOH . I 5 HOH A 38 638 638 HOH HOH . I 5 HOH A 39 639 639 HOH HOH . I 5 HOH A 40 640 640 HOH HOH . I 5 HOH A 41 641 641 HOH HOH . I 5 HOH A 42 642 642 HOH HOH . I 5 HOH A 43 643 643 HOH HOH . I 5 HOH A 44 644 644 HOH HOH . I 5 HOH A 45 645 645 HOH HOH . I 5 HOH A 46 646 646 HOH HOH . I 5 HOH A 47 647 647 HOH HOH . I 5 HOH A 48 648 648 HOH HOH . I 5 HOH A 49 649 649 HOH HOH . I 5 HOH A 50 650 650 HOH HOH . I 5 HOH A 51 651 651 HOH HOH . I 5 HOH A 52 652 652 HOH HOH . I 5 HOH A 53 653 653 HOH HOH . I 5 HOH A 54 654 654 HOH HOH . I 5 HOH A 55 655 655 HOH HOH . I 5 HOH A 56 656 656 HOH HOH . I 5 HOH A 57 657 657 HOH HOH . I 5 HOH A 58 658 658 HOH HOH . I 5 HOH A 59 659 659 HOH HOH . I 5 HOH A 60 660 660 HOH HOH . I 5 HOH A 61 661 661 HOH HOH . I 5 HOH A 62 662 662 HOH HOH . I 5 HOH A 63 663 663 HOH HOH . I 5 HOH A 64 664 664 HOH HOH . I 5 HOH A 65 665 665 HOH HOH . I 5 HOH A 66 666 666 HOH HOH . I 5 HOH A 67 667 667 HOH HOH . I 5 HOH A 68 668 668 HOH HOH . I 5 HOH A 69 669 669 HOH HOH . I 5 HOH A 70 670 670 HOH HOH . I 5 HOH A 71 671 671 HOH HOH . I 5 HOH A 72 672 672 HOH HOH . I 5 HOH A 73 673 673 HOH HOH . I 5 HOH A 74 674 674 HOH HOH . I 5 HOH A 75 675 675 HOH HOH . I 5 HOH A 76 676 676 HOH HOH . I 5 HOH A 77 677 677 HOH HOH . I 5 HOH A 78 678 678 HOH HOH . I 5 HOH A 79 679 679 HOH HOH . I 5 HOH A 80 680 680 HOH HOH . I 5 HOH A 81 681 681 HOH HOH . I 5 HOH A 82 682 682 HOH HOH . I 5 HOH A 83 683 683 HOH HOH . I 5 HOH A 84 684 684 HOH HOH . I 5 HOH A 85 685 685 HOH HOH . I 5 HOH A 86 686 686 HOH HOH . I 5 HOH A 87 687 687 HOH HOH . I 5 HOH A 88 688 688 HOH HOH . I 5 HOH A 89 689 689 HOH HOH . I 5 HOH A 90 690 690 HOH HOH . I 5 HOH A 91 691 691 HOH HOH . I 5 HOH A 92 692 692 HOH HOH . I 5 HOH A 93 693 693 HOH HOH . I 5 HOH A 94 694 694 HOH HOH . I 5 HOH A 95 695 695 HOH HOH . I 5 HOH A 96 696 696 HOH HOH . I 5 HOH A 97 697 697 HOH HOH . I 5 HOH A 98 698 698 HOH HOH . I 5 HOH A 99 699 699 HOH HOH . I 5 HOH A 100 700 700 HOH HOH . I 5 HOH A 101 701 701 HOH HOH . I 5 HOH A 102 702 702 HOH HOH . I 5 HOH A 103 703 703 HOH HOH . I 5 HOH A 104 704 704 HOH HOH . I 5 HOH A 105 705 705 HOH HOH . I 5 HOH A 106 706 706 HOH HOH . I 5 HOH A 107 707 707 HOH HOH . I 5 HOH A 108 708 708 HOH HOH . I 5 HOH A 109 709 709 HOH HOH . I 5 HOH A 110 710 710 HOH HOH . I 5 HOH A 111 711 711 HOH HOH . J 5 HOH B 1 601 601 HOH HOH . J 5 HOH B 2 602 602 HOH HOH . J 5 HOH B 3 603 603 HOH HOH . J 5 HOH B 4 604 604 HOH HOH . J 5 HOH B 5 605 605 HOH HOH . J 5 HOH B 6 606 606 HOH HOH . J 5 HOH B 7 607 607 HOH HOH . J 5 HOH B 8 608 608 HOH HOH . J 5 HOH B 9 609 609 HOH HOH . J 5 HOH B 10 610 610 HOH HOH . J 5 HOH B 11 611 611 HOH HOH . J 5 HOH B 12 612 612 HOH HOH . J 5 HOH B 13 613 613 HOH HOH . J 5 HOH B 14 614 614 HOH HOH . J 5 HOH B 15 615 615 HOH HOH . J 5 HOH B 16 616 616 HOH HOH . J 5 HOH B 17 617 617 HOH HOH . J 5 HOH B 18 618 618 HOH HOH . J 5 HOH B 19 619 619 HOH HOH . J 5 HOH B 20 620 620 HOH HOH . J 5 HOH B 21 621 621 HOH HOH . J 5 HOH B 22 622 622 HOH HOH . J 5 HOH B 23 623 623 HOH HOH . J 5 HOH B 24 624 624 HOH HOH . J 5 HOH B 25 625 625 HOH HOH . J 5 HOH B 26 626 626 HOH HOH . J 5 HOH B 27 627 627 HOH HOH . J 5 HOH B 28 628 628 HOH HOH . J 5 HOH B 29 629 629 HOH HOH . J 5 HOH B 30 630 630 HOH HOH . J 5 HOH B 31 631 631 HOH HOH . J 5 HOH B 32 632 632 HOH HOH . J 5 HOH B 33 633 633 HOH HOH . J 5 HOH B 34 634 634 HOH HOH . J 5 HOH B 35 635 635 HOH HOH . J 5 HOH B 36 636 636 HOH HOH . J 5 HOH B 37 637 637 HOH HOH . J 5 HOH B 38 638 638 HOH HOH . J 5 HOH B 39 639 639 HOH HOH . J 5 HOH B 40 640 640 HOH HOH . J 5 HOH B 41 641 641 HOH HOH . J 5 HOH B 42 642 642 HOH HOH . J 5 HOH B 43 643 643 HOH HOH . J 5 HOH B 44 644 644 HOH HOH . J 5 HOH B 45 645 645 HOH HOH . J 5 HOH B 46 646 646 HOH HOH . J 5 HOH B 47 647 647 HOH HOH . J 5 HOH B 48 648 648 HOH HOH . J 5 HOH B 49 649 649 HOH HOH . J 5 HOH B 50 650 650 HOH HOH . J 5 HOH B 51 651 651 HOH HOH . J 5 HOH B 52 652 652 HOH HOH . J 5 HOH B 53 653 653 HOH HOH . J 5 HOH B 54 654 654 HOH HOH . J 5 HOH B 55 655 655 HOH HOH . J 5 HOH B 56 656 656 HOH HOH . J 5 HOH B 57 657 657 HOH HOH . J 5 HOH B 58 658 658 HOH HOH . J 5 HOH B 59 659 659 HOH HOH . J 5 HOH B 60 660 660 HOH HOH . J 5 HOH B 61 661 661 HOH HOH . J 5 HOH B 62 662 662 HOH HOH . J 5 HOH B 63 663 663 HOH HOH . J 5 HOH B 64 664 664 HOH HOH . J 5 HOH B 65 665 665 HOH HOH . J 5 HOH B 66 666 666 HOH HOH . J 5 HOH B 67 667 667 HOH HOH . J 5 HOH B 68 668 668 HOH HOH . J 5 HOH B 69 669 669 HOH HOH . J 5 HOH B 70 670 670 HOH HOH . J 5 HOH B 71 671 671 HOH HOH . J 5 HOH B 72 672 672 HOH HOH . J 5 HOH B 73 673 673 HOH HOH . J 5 HOH B 74 674 674 HOH HOH . J 5 HOH B 75 675 675 HOH HOH . J 5 HOH B 76 676 676 HOH HOH . J 5 HOH B 77 677 677 HOH HOH . J 5 HOH B 78 678 678 HOH HOH . J 5 HOH B 79 679 679 HOH HOH . J 5 HOH B 80 680 680 HOH HOH . J 5 HOH B 81 681 681 HOH HOH . J 5 HOH B 82 682 682 HOH HOH . J 5 HOH B 83 683 683 HOH HOH . J 5 HOH B 84 684 684 HOH HOH . J 5 HOH B 85 685 685 HOH HOH . J 5 HOH B 86 686 686 HOH HOH . J 5 HOH B 87 687 687 HOH HOH . J 5 HOH B 88 688 688 HOH HOH . J 5 HOH B 89 689 689 HOH HOH . J 5 HOH B 90 690 690 HOH HOH . J 5 HOH B 91 691 691 HOH HOH . J 5 HOH B 92 692 692 HOH HOH . J 5 HOH B 93 693 693 HOH HOH . J 5 HOH B 94 694 694 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 ICT . . . D 3 38.814 -66.614 17.147 1 20 ? C1 ICT 502 A 1 HETATM 2 O O1 ICT . . . D 3 38.301 -66.818 16.081 1 20 ? O1 ICT 502 A 1 HETATM 3 O O2 ICT . . . D 3 38.451 -67.365 18.005 1 20 ? O2 ICT 502 A 1 HETATM 4 C C2 ICT . . . D 3 39.808 -65.536 17.397 1 20 ? C2 ICT 502 A 1 HETATM 5 O O7 ICT . . . D 3 40.213 -65.544 18.714 1 20 ? O7 ICT 502 A 1 HETATM 6 C C3 ICT . . . D 3 39.26 -64.334 16.677 1 20 ? C3 ICT 502 A 1 HETATM 7 C C4 ICT . . . D 3 40.083 -63.662 15.603 1 20 ? C4 ICT 502 A 1 HETATM 8 C C5 ICT . . . D 3 39.606 -62.512 14.77 1 20 ? C5 ICT 502 A 1 HETATM 9 O O3 ICT . . . D 3 38.633 -62.49 14.046 1 20 ? O3 ICT 502 A 1 HETATM 10 O O4 ICT . . . D 3 40.249 -61.494 14.747 1 20 ? O4 ICT 502 A 1 HETATM 11 C C6 ICT . . . D 3 38.16 -63.585 17.314 1 20 ? C6 ICT 502 A 1 HETATM 12 O O5 ICT . . . D 3 37.053 -64.076 17.26 1 20 ? O5 ICT 502 A 1 HETATM 13 O O6 ICT . . . D 3 38.289 -62.549 17.901 1 20 ? O6 ICT 502 A 1 HETATM 14 H H2 ICT . . . D 3 40.599 -65.798 16.886 1 20 ? H2 ICT 502 A 1 HETATM 15 H HO7 ICT . . . D 3 40.941 -65.068 18.797 1 20 ? HO7 ICT 502 A 1 HETATM 16 H H3 ICT . . . D 3 38.694 -64.837 16.063 1 20 ? H3 ICT 502 A 1 HETATM 17 H H41 ICT . . . D 3 40.335 -64.358 14.982 1 20 ? H41 ICT 502 A 1 HETATM 18 H H42 ICT . . . D 3 40.904 -63.363 16.038 1 20 ? H42 ICT 502 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 18 #