data_6YW4 # _model_server_result.job_id 1UtevIx50-bspxX5ANhY1w _model_server_result.datetime_utc '2024-10-19 09:19:10' _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 6yw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6YW4 # _exptl.entry_id 6YW4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.086 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OXALYLGLYCINE _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 120 _cell.entry_id 6YW4 _cell.length_a 46.622 _cell.length_b 46.622 _cell.length_c 203.711 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YW4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 B C09 48V 1 B 48V 0 1_555 B N DTY 2 B DTY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B N01 48V 1 B 48V 0 1_555 B C THR 14 B THR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale3 B C DTY 2 B DTY 1 1_555 B N VAL 3 B VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? metalc ? metalc1 A NE2 HIS 139 A HIS 313 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A OD1 ASP 141 A ASP 315 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc3 A NE2 HIS 200 A HIS 374 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc4 C MN MN . A MN 501 1_555 D O1 OGA . A OGA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc5 C MN MN . A MN 501 1_555 D O2' OGA . A OGA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 C MN MN . A MN 501 1_555 G O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? # _chem_comp.formula 'C4 H5 N O5' _chem_comp.formula_weight 147.086 _chem_comp.id OGA _chem_comp.mon_nstd_flag . _chem_comp.name N-OXALYLGLYCINE _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 C2 OGA sing 281 n n C1 O1 OGA doub 282 n n C1 O2 OGA sing 283 n n C2 O2' OGA doub 284 n n C2 N1 OGA sing 285 n n C4 C5 OGA sing 286 n n C4 N1 OGA sing 287 n n C4 H4C1 OGA sing 288 n n C4 H4C2 OGA sing 289 n n C5 O3 OGA sing 290 n n C5 O4 OGA doub 291 n n O2 H2 OGA sing 292 n n O3 H3 OGA sing 293 n n N1 H1 OGA sing 294 n n # _atom_sites.entry_id 6YW4 _atom_sites.fract_transf_matrix[1][1] 0.021449 _atom_sites.fract_transf_matrix[1][2] 0.012384 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024767 _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] 0.004909 _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 MN A 1 501 501 MN MN . D 4 OGA A 1 502 601 OGA OGA . E 5 SO4 A 1 503 701 SO4 SO4 . F 5 SO4 A 1 504 702 SO4 SO4 . G 6 HOH A 1 601 97 HOH HOH . G 6 HOH A 2 602 101 HOH HOH . G 6 HOH A 3 603 104 HOH HOH . G 6 HOH A 4 604 130 HOH HOH . G 6 HOH A 5 605 48 HOH HOH . G 6 HOH A 6 606 163 HOH HOH . G 6 HOH A 7 607 185 HOH HOH . G 6 HOH A 8 608 88 HOH HOH . G 6 HOH A 9 609 134 HOH HOH . G 6 HOH A 10 610 95 HOH HOH . G 6 HOH A 11 611 94 HOH HOH . G 6 HOH A 12 612 73 HOH HOH . G 6 HOH A 13 613 82 HOH HOH . G 6 HOH A 14 614 27 HOH HOH . G 6 HOH A 15 615 8 HOH HOH . G 6 HOH A 16 616 125 HOH HOH . G 6 HOH A 17 617 85 HOH HOH . G 6 HOH A 18 618 174 HOH HOH . G 6 HOH A 19 619 191 HOH HOH . G 6 HOH A 20 620 10 HOH HOH . G 6 HOH A 21 621 121 HOH HOH . G 6 HOH A 22 622 107 HOH HOH . G 6 HOH A 23 623 29 HOH HOH . G 6 HOH A 24 624 26 HOH HOH . G 6 HOH A 25 625 153 HOH HOH . G 6 HOH A 26 626 126 HOH HOH . G 6 HOH A 27 627 122 HOH HOH . G 6 HOH A 28 628 41 HOH HOH . G 6 HOH A 29 629 113 HOH HOH . G 6 HOH A 30 630 167 HOH HOH . G 6 HOH A 31 631 5 HOH HOH . G 6 HOH A 32 632 21 HOH HOH . G 6 HOH A 33 633 91 HOH HOH . G 6 HOH A 34 634 25 HOH HOH . G 6 HOH A 35 635 11 HOH HOH . G 6 HOH A 36 636 100 HOH HOH . G 6 HOH A 37 637 150 HOH HOH . G 6 HOH A 38 638 165 HOH HOH . G 6 HOH A 39 639 103 HOH HOH . G 6 HOH A 40 640 78 HOH HOH . G 6 HOH A 41 641 57 HOH HOH . G 6 HOH A 42 642 117 HOH HOH . G 6 HOH A 43 643 132 HOH HOH . G 6 HOH A 44 644 131 HOH HOH . G 6 HOH A 45 645 4 HOH HOH . G 6 HOH A 46 646 89 HOH HOH . G 6 HOH A 47 647 86 HOH HOH . G 6 HOH A 48 648 181 HOH HOH . G 6 HOH A 49 649 84 HOH HOH . G 6 HOH A 50 650 75 HOH HOH . G 6 HOH A 51 651 192 HOH HOH . G 6 HOH A 52 652 54 HOH HOH . G 6 HOH A 53 653 90 HOH HOH . G 6 HOH A 54 654 106 HOH HOH . G 6 HOH A 55 655 61 HOH HOH . G 6 HOH A 56 656 110 HOH HOH . G 6 HOH A 57 657 159 HOH HOH . G 6 HOH A 58 658 24 HOH HOH . G 6 HOH A 59 659 58 HOH HOH . G 6 HOH A 60 660 23 HOH HOH . G 6 HOH A 61 661 175 HOH HOH . G 6 HOH A 62 662 3 HOH HOH . G 6 HOH A 63 663 182 HOH HOH . G 6 HOH A 64 664 66 HOH HOH . G 6 HOH A 65 665 6 HOH HOH . G 6 HOH A 66 666 2 HOH HOH . G 6 HOH A 67 667 56 HOH HOH . G 6 HOH A 68 668 1 HOH HOH . G 6 HOH A 69 669 127 HOH HOH . G 6 HOH A 70 670 20 HOH HOH . G 6 HOH A 71 671 34 HOH HOH . G 6 HOH A 72 672 120 HOH HOH . G 6 HOH A 73 673 30 HOH HOH . G 6 HOH A 74 674 79 HOH HOH . G 6 HOH A 75 675 7 HOH HOH . G 6 HOH A 76 676 114 HOH HOH . G 6 HOH A 77 677 12 HOH HOH . G 6 HOH A 78 678 62 HOH HOH . G 6 HOH A 79 679 180 HOH HOH . G 6 HOH A 80 680 80 HOH HOH . G 6 HOH A 81 681 64 HOH HOH . G 6 HOH A 82 682 59 HOH HOH . G 6 HOH A 83 683 67 HOH HOH . G 6 HOH A 84 684 166 HOH HOH . G 6 HOH A 85 685 77 HOH HOH . G 6 HOH A 86 686 53 HOH HOH . G 6 HOH A 87 687 19 HOH HOH . G 6 HOH A 88 688 98 HOH HOH . G 6 HOH A 89 689 124 HOH HOH . G 6 HOH A 90 690 40 HOH HOH . G 6 HOH A 91 691 138 HOH HOH . G 6 HOH A 92 692 42 HOH HOH . G 6 HOH A 93 693 168 HOH HOH . G 6 HOH A 94 694 123 HOH HOH . G 6 HOH A 95 695 47 HOH HOH . G 6 HOH A 96 696 60 HOH HOH . G 6 HOH A 97 697 160 HOH HOH . G 6 HOH A 98 698 17 HOH HOH . G 6 HOH A 99 699 31 HOH HOH . G 6 HOH A 100 700 147 HOH HOH . G 6 HOH A 101 701 36 HOH HOH . G 6 HOH A 102 702 177 HOH HOH . G 6 HOH A 103 703 35 HOH HOH . G 6 HOH A 104 704 9 HOH HOH . G 6 HOH A 105 705 173 HOH HOH . G 6 HOH A 106 706 72 HOH HOH . G 6 HOH A 107 707 118 HOH HOH . G 6 HOH A 108 708 154 HOH HOH . G 6 HOH A 109 709 13 HOH HOH . G 6 HOH A 110 710 152 HOH HOH . G 6 HOH A 111 711 108 HOH HOH . G 6 HOH A 112 712 33 HOH HOH . G 6 HOH A 113 713 111 HOH HOH . G 6 HOH A 114 714 16 HOH HOH . G 6 HOH A 115 715 70 HOH HOH . G 6 HOH A 116 716 32 HOH HOH . G 6 HOH A 117 717 188 HOH HOH . G 6 HOH A 118 718 116 HOH HOH . G 6 HOH A 119 719 45 HOH HOH . G 6 HOH A 120 720 189 HOH HOH . G 6 HOH A 121 721 52 HOH HOH . G 6 HOH A 122 722 15 HOH HOH . G 6 HOH A 123 723 112 HOH HOH . G 6 HOH A 124 724 158 HOH HOH . G 6 HOH A 125 725 183 HOH HOH . G 6 HOH A 126 726 93 HOH HOH . G 6 HOH A 127 727 28 HOH HOH . G 6 HOH A 128 728 49 HOH HOH . G 6 HOH A 129 729 71 HOH HOH . G 6 HOH A 130 730 99 HOH HOH . G 6 HOH A 131 731 142 HOH HOH . G 6 HOH A 132 732 50 HOH HOH . G 6 HOH A 133 733 44 HOH HOH . G 6 HOH A 134 734 170 HOH HOH . G 6 HOH A 135 735 39 HOH HOH . G 6 HOH A 136 736 43 HOH HOH . G 6 HOH A 137 737 169 HOH HOH . G 6 HOH A 138 738 162 HOH HOH . G 6 HOH A 139 739 51 HOH HOH . G 6 HOH A 140 740 136 HOH HOH . G 6 HOH A 141 741 119 HOH HOH . G 6 HOH A 142 742 145 HOH HOH . G 6 HOH A 143 743 172 HOH HOH . G 6 HOH A 144 744 193 HOH HOH . G 6 HOH A 145 745 105 HOH HOH . G 6 HOH A 146 746 194 HOH HOH . G 6 HOH A 147 747 141 HOH HOH . G 6 HOH A 148 748 63 HOH HOH . G 6 HOH A 149 749 157 HOH HOH . G 6 HOH A 150 750 186 HOH HOH . G 6 HOH A 151 751 92 HOH HOH . G 6 HOH A 152 752 68 HOH HOH . G 6 HOH A 153 753 46 HOH HOH . G 6 HOH A 154 754 74 HOH HOH . G 6 HOH A 155 755 195 HOH HOH . G 6 HOH A 156 756 179 HOH HOH . G 6 HOH A 157 757 135 HOH HOH . G 6 HOH A 158 758 102 HOH HOH . G 6 HOH A 159 759 38 HOH HOH . G 6 HOH A 160 760 129 HOH HOH . G 6 HOH A 161 761 139 HOH HOH . G 6 HOH A 162 762 76 HOH HOH . G 6 HOH A 163 763 164 HOH HOH . G 6 HOH A 164 764 55 HOH HOH . G 6 HOH A 165 765 81 HOH HOH . G 6 HOH A 166 766 128 HOH HOH . G 6 HOH A 167 767 115 HOH HOH . G 6 HOH A 168 768 143 HOH HOH . G 6 HOH A 169 769 146 HOH HOH . G 6 HOH A 170 770 133 HOH HOH . G 6 HOH A 171 771 156 HOH HOH . G 6 HOH A 172 772 171 HOH HOH . G 6 HOH A 173 773 190 HOH HOH . G 6 HOH A 174 774 137 HOH HOH . G 6 HOH A 175 775 178 HOH HOH . G 6 HOH A 176 776 149 HOH HOH . G 6 HOH A 177 777 151 HOH HOH . G 6 HOH A 178 778 109 HOH HOH . G 6 HOH A 179 779 155 HOH HOH . G 6 HOH A 180 780 161 HOH HOH . H 6 HOH B 1 101 22 HOH HOH . H 6 HOH B 2 102 83 HOH HOH . H 6 HOH B 3 103 14 HOH HOH . H 6 HOH B 4 104 69 HOH HOH . H 6 HOH B 5 105 148 HOH HOH . H 6 HOH B 6 106 176 HOH HOH . H 6 HOH B 7 107 65 HOH HOH . H 6 HOH B 8 108 18 HOH HOH . H 6 HOH B 9 109 140 HOH HOH . H 6 HOH B 10 110 96 HOH HOH . H 6 HOH B 11 111 144 HOH HOH . H 6 HOH B 12 112 87 HOH HOH . H 6 HOH B 13 113 37 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 OGA . . . D 4 -8.625 15.56 -7.753 1 20.38 ? C1 OGA 502 A 1 HETATM 2 C C2 OGA . . . D 4 -9.161 16.003 -6.367 1 16.79 ? C2 OGA 502 A 1 HETATM 3 C C4 OGA . . . D 4 -10.001 15.508 -4.171 1 19.42 ? C4 OGA 502 A 1 HETATM 4 C C5 OGA . . . D 4 -9.777 14.616 -3.035 1 18.73 ? C5 OGA 502 A 1 HETATM 5 O O1 OGA . . . D 4 -8.966 16.248 -8.743 1 21.13 ? O1 OGA 502 A 1 HETATM 6 O O2 OGA . . . D 4 -7.854 14.538 -7.763 1 23.56 ? O2 OGA 502 A 1 HETATM 7 O O2' OGA . . . D 4 -9.56 17.279 -6.363 1 18.48 ? O2' OGA 502 A 1 HETATM 8 O O3 OGA . . . D 4 -10.464 14.844 -1.99 1 19.49 ? O3 OGA 502 A 1 HETATM 9 N N1 OGA . . . D 4 -9.201 15.178 -5.332 1 19.63 ? N1 OGA 502 A 1 HETATM 10 O O4 OGA . . . D 4 -8.954 13.657 -3.112 1 21.21 ? O4 OGA 502 A 1 HETATM 11 H H4C1 OGA . . . D 4 -9.784 16.419 -3.895 1 23.31 ? H4C1 OGA 502 A 1 HETATM 12 H H4C2 OGA . . . D 4 -10.943 15.46 -4.421 1 23.31 ? H4C2 OGA 502 A 1 HETATM 13 H H1 OGA . . . D 4 -8.746 14.389 -5.294 1 23.56 ? H1 OGA 502 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #