data_1DDR # _model_server_result.job_id 31yzaJAMrGEYGerv4ooWIg _model_server_result.datetime_utc '2024-11-06 03:03:58' _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 1ddr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":200}' # _entry.id 1DDR # _exptl.entry_id 1DDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.439 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHOTREXATE _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 90 _cell.angle_gamma 120 _cell.entry_id 1DDR _cell.length_a 93.181 _cell.length_b 93.185 _cell.length_c 73.886 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _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,K,L,M,N _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 J 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 OD1 ASN 18 A ASN 18 2_665 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc2 B O SER 135 B SER 135 1_555 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? metalc ? metalc3 B O ALA 143 B ALA 143 2_665 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 I CA CA . B CA 203 1_555 N O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? # _chem_comp.formula 'C20 H22 N8 O5' _chem_comp.formula_weight 454.439 _chem_comp.id MTX _chem_comp.mon_nstd_flag . _chem_comp.name METHOTREXATE _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 N1 C2 MTX doub 237 n y N1 C8A MTX sing 238 n y C2 NA2 MTX sing 239 n n C2 N3 MTX sing 240 n y NA2 HN21 MTX sing 241 n n NA2 HN22 MTX sing 242 n n N3 C4 MTX doub 243 n y C4 NA4 MTX sing 244 n n C4 C4A MTX sing 245 n y NA4 HN41 MTX sing 246 n n NA4 HN42 MTX sing 247 n n C4A N5 MTX sing 248 n y C4A C8A MTX doub 249 n y N5 C6 MTX doub 250 n y C6 C7 MTX sing 251 n y C6 C9 MTX sing 252 n n C7 N8 MTX doub 253 n y C7 H7 MTX sing 254 n n N8 C8A MTX sing 255 n y C9 N10 MTX sing 256 n n C9 H91 MTX sing 257 n n C9 H92 MTX sing 258 n n N10 CM MTX sing 259 n n N10 C14 MTX sing 260 n n CM HM1 MTX sing 261 n n CM HM2 MTX sing 262 n n CM HM3 MTX sing 263 n n C11 C12 MTX doub 264 n y C11 C16 MTX sing 265 n y C11 C MTX sing 266 n n C12 C13 MTX sing 267 n y C12 H12 MTX sing 268 n n C13 C14 MTX doub 269 n y C13 H13 MTX sing 270 n n C14 C15 MTX sing 271 n y C15 C16 MTX doub 272 n y C15 H15 MTX sing 273 n n C16 H16 MTX sing 274 n n C O MTX doub 275 n n C N MTX sing 276 n n N CA MTX sing 277 n n N HN MTX sing 278 n n CA CT MTX sing 279 n n CA CB MTX sing 280 n n CA HA MTX sing 281 n n CT O1 MTX doub 282 n n CT O2 MTX sing 283 n n O2 HO2 MTX sing 284 n n CB CG MTX sing 285 n n CB HB1 MTX sing 286 n n CB HB2 MTX sing 287 n n CG CD MTX sing 288 n n CG HG1 MTX sing 289 n n CG HG2 MTX sing 290 n n CD OE1 MTX doub 291 n n CD OE2 MTX sing 292 n n OE2 HOE2 MTX sing 293 n n # _atom_sites.entry_id 1DDR _atom_sites.fract_transf_matrix[1][1] 0.010732 _atom_sites.fract_transf_matrix[1][2] 0.006196 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012391 _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] 0.013534 _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 CL A 1 201 201 CL CL . D 3 MTX A 1 200 200 MTX MTX . E 4 URE A 1 211 211 URE URE . F 4 URE A 1 212 212 URE URE . G 4 URE A 1 213 213 URE URE . H 2 CL B 1 202 202 CL CL . I 5 CA B 1 203 203 CA CA . J 3 MTX B 1 200 200 MTX MTX . K 4 URE B 1 214 214 URE URE . L 4 URE B 1 215 215 URE URE . M 6 HOH A 1 701 701 HOH HOH . M 6 HOH A 2 702 702 HOH HOH . M 6 HOH A 3 703 703 HOH HOH . M 6 HOH A 4 704 704 HOH HOH . M 6 HOH A 5 705 705 HOH HOH . M 6 HOH A 6 706 706 HOH HOH . M 6 HOH A 7 707 707 HOH HOH . M 6 HOH A 8 708 708 HOH HOH . M 6 HOH A 9 709 709 HOH HOH . M 6 HOH A 10 710 710 HOH HOH . M 6 HOH A 11 711 711 HOH HOH . M 6 HOH A 12 712 712 HOH HOH . M 6 HOH A 13 713 713 HOH HOH . M 6 HOH A 14 714 714 HOH HOH . M 6 HOH A 15 715 715 HOH HOH . M 6 HOH A 16 716 716 HOH HOH . M 6 HOH A 17 717 717 HOH HOH . M 6 HOH A 18 718 718 HOH HOH . M 6 HOH A 19 719 719 HOH HOH . M 6 HOH A 20 720 720 HOH HOH . M 6 HOH A 21 721 721 HOH HOH . M 6 HOH A 22 722 722 HOH HOH . M 6 HOH A 23 723 723 HOH HOH . M 6 HOH A 24 724 724 HOH HOH . M 6 HOH A 25 725 725 HOH HOH . M 6 HOH A 26 727 727 HOH HOH . M 6 HOH A 27 728 728 HOH HOH . M 6 HOH A 28 729 729 HOH HOH . M 6 HOH A 29 730 730 HOH HOH . M 6 HOH A 30 731 731 HOH HOH . M 6 HOH A 31 732 732 HOH HOH . M 6 HOH A 32 734 734 HOH HOH . M 6 HOH A 33 735 735 HOH HOH . M 6 HOH A 34 736 736 HOH HOH . M 6 HOH A 35 737 737 HOH HOH . M 6 HOH A 36 738 738 HOH HOH . M 6 HOH A 37 739 739 HOH HOH . M 6 HOH A 38 740 740 HOH HOH . M 6 HOH A 39 741 741 HOH HOH . M 6 HOH A 40 742 742 HOH HOH . M 6 HOH A 41 753 753 HOH HOH . M 6 HOH A 42 780 780 HOH HOH . M 6 HOH A 43 781 781 HOH HOH . M 6 HOH A 44 782 782 HOH HOH . M 6 HOH A 45 783 783 HOH HOH . M 6 HOH A 46 788 788 HOH HOH . M 6 HOH A 47 794 794 HOH HOH . M 6 HOH A 48 795 795 HOH HOH . M 6 HOH A 49 796 796 HOH HOH . M 6 HOH A 50 797 797 HOH HOH . M 6 HOH A 51 798 798 HOH HOH . M 6 HOH A 52 799 799 HOH HOH . M 6 HOH A 53 800 800 HOH HOH . M 6 HOH A 54 801 801 HOH HOH . M 6 HOH A 55 802 802 HOH HOH . M 6 HOH A 56 804 804 HOH HOH . M 6 HOH A 57 805 805 HOH HOH . M 6 HOH A 58 806 806 HOH HOH . M 6 HOH A 59 807 807 HOH HOH . M 6 HOH A 60 809 809 HOH HOH . M 6 HOH A 61 810 810 HOH HOH . M 6 HOH A 62 811 811 HOH HOH . M 6 HOH A 63 812 812 HOH HOH . M 6 HOH A 64 814 814 HOH HOH . M 6 HOH A 65 815 815 HOH HOH . M 6 HOH A 66 816 816 HOH HOH . M 6 HOH A 67 817 817 HOH HOH . M 6 HOH A 68 818 818 HOH HOH . M 6 HOH A 69 819 819 HOH HOH . M 6 HOH A 70 820 820 HOH HOH . M 6 HOH A 71 821 821 HOH HOH . M 6 HOH A 72 822 822 HOH HOH . M 6 HOH A 73 823 823 HOH HOH . M 6 HOH A 74 824 824 HOH HOH . M 6 HOH A 75 825 825 HOH HOH . M 6 HOH A 76 826 826 HOH HOH . M 6 HOH A 77 827 827 HOH HOH . M 6 HOH A 78 828 828 HOH HOH . M 6 HOH A 79 829 829 HOH HOH . M 6 HOH A 80 830 830 HOH HOH . M 6 HOH A 81 833 833 HOH HOH . M 6 HOH A 82 834 834 HOH HOH . M 6 HOH A 83 835 835 HOH HOH . M 6 HOH A 84 836 836 HOH HOH . M 6 HOH A 85 837 837 HOH HOH . M 6 HOH A 86 838 838 HOH HOH . M 6 HOH A 87 839 839 HOH HOH . M 6 HOH A 88 840 840 HOH HOH . M 6 HOH A 89 860 860 HOH HOH . M 6 HOH A 90 861 861 HOH HOH . M 6 HOH A 91 862 862 HOH HOH . M 6 HOH A 92 863 863 HOH HOH . M 6 HOH A 93 864 864 HOH HOH . M 6 HOH A 94 868 868 HOH HOH . M 6 HOH A 95 875 875 HOH HOH . M 6 HOH A 96 876 876 HOH HOH . M 6 HOH A 97 877 877 HOH HOH . M 6 HOH A 98 878 878 HOH HOH . M 6 HOH A 99 879 879 HOH HOH . M 6 HOH A 100 880 880 HOH HOH . M 6 HOH A 101 881 881 HOH HOH . M 6 HOH A 102 882 882 HOH HOH . N 6 HOH B 1 733 733 HOH HOH . N 6 HOH B 2 743 743 HOH HOH . N 6 HOH B 3 744 744 HOH HOH . N 6 HOH B 4 745 745 HOH HOH . N 6 HOH B 5 746 746 HOH HOH . N 6 HOH B 6 747 747 HOH HOH . N 6 HOH B 7 748 748 HOH HOH . N 6 HOH B 8 749 749 HOH HOH . N 6 HOH B 9 750 750 HOH HOH . N 6 HOH B 10 751 751 HOH HOH . N 6 HOH B 11 752 752 HOH HOH . N 6 HOH B 12 754 754 HOH HOH . N 6 HOH B 13 756 756 HOH HOH . N 6 HOH B 14 757 757 HOH HOH . N 6 HOH B 15 758 758 HOH HOH . N 6 HOH B 16 759 759 HOH HOH . N 6 HOH B 17 760 760 HOH HOH . N 6 HOH B 18 761 761 HOH HOH . N 6 HOH B 19 762 762 HOH HOH . N 6 HOH B 20 763 763 HOH HOH . N 6 HOH B 21 764 764 HOH HOH . N 6 HOH B 22 765 765 HOH HOH . N 6 HOH B 23 766 766 HOH HOH . N 6 HOH B 24 767 767 HOH HOH . N 6 HOH B 25 768 768 HOH HOH . N 6 HOH B 26 769 769 HOH HOH . N 6 HOH B 27 770 770 HOH HOH . N 6 HOH B 28 771 771 HOH HOH . N 6 HOH B 29 772 772 HOH HOH . N 6 HOH B 30 773 773 HOH HOH . N 6 HOH B 31 774 774 HOH HOH . N 6 HOH B 32 775 775 HOH HOH . N 6 HOH B 33 776 776 HOH HOH . N 6 HOH B 34 777 777 HOH HOH . N 6 HOH B 35 778 778 HOH HOH . N 6 HOH B 36 779 779 HOH HOH . N 6 HOH B 37 784 784 HOH HOH . N 6 HOH B 38 785 785 HOH HOH . N 6 HOH B 39 786 786 HOH HOH . N 6 HOH B 40 787 787 HOH HOH . N 6 HOH B 41 789 789 HOH HOH . N 6 HOH B 42 790 790 HOH HOH . N 6 HOH B 43 791 791 HOH HOH . N 6 HOH B 44 792 792 HOH HOH . N 6 HOH B 45 793 793 HOH HOH . N 6 HOH B 46 803 803 HOH HOH . N 6 HOH B 47 808 808 HOH HOH . N 6 HOH B 48 813 813 HOH HOH . N 6 HOH B 49 831 831 HOH HOH . N 6 HOH B 50 832 832 HOH HOH . N 6 HOH B 51 841 841 HOH HOH . N 6 HOH B 52 842 842 HOH HOH . N 6 HOH B 53 843 843 HOH HOH . N 6 HOH B 54 844 844 HOH HOH . N 6 HOH B 55 845 845 HOH HOH . N 6 HOH B 56 846 846 HOH HOH . N 6 HOH B 57 847 847 HOH HOH . N 6 HOH B 58 848 848 HOH HOH . N 6 HOH B 59 849 849 HOH HOH . N 6 HOH B 60 850 850 HOH HOH . N 6 HOH B 61 851 851 HOH HOH . N 6 HOH B 62 852 852 HOH HOH . N 6 HOH B 63 854 854 HOH HOH . N 6 HOH B 64 855 855 HOH HOH . N 6 HOH B 65 856 856 HOH HOH . N 6 HOH B 66 857 857 HOH HOH . N 6 HOH B 67 858 858 HOH HOH . N 6 HOH B 68 859 859 HOH HOH . N 6 HOH B 69 865 865 HOH HOH . N 6 HOH B 70 866 866 HOH HOH . N 6 HOH B 71 867 867 HOH HOH . N 6 HOH B 72 869 869 HOH HOH . N 6 HOH B 73 870 870 HOH HOH . N 6 HOH B 74 871 871 HOH HOH . N 6 HOH B 75 872 872 HOH HOH . N 6 HOH B 76 873 873 HOH HOH . N 6 HOH B 77 874 874 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 N N1 MTX . . . D 3 22.884 58.684 24.048 1 4.11 ? N1 MTX 200 A 1 HETATM 2 C C2 MTX . . . D 3 23.488 58.193 22.928 1 2 ? C2 MTX 200 A 1 HETATM 3 N NA2 MTX . . . D 3 24.868 58.079 22.827 1 4.22 ? NA2 MTX 200 A 1 HETATM 4 N N3 MTX . . . D 3 22.737 57.78 21.885 1 2 ? N3 MTX 200 A 1 HETATM 5 C C4 MTX . . . D 3 21.365 57.771 21.755 1 2 ? C4 MTX 200 A 1 HETATM 6 N NA4 MTX . . . D 3 20.676 57.26 20.632 1 2 ? NA4 MTX 200 A 1 HETATM 7 C C4A MTX . . . D 3 20.73 58.293 22.932 1 2 ? C4A MTX 200 A 1 HETATM 8 N N5 MTX . . . D 3 19.374 58.348 22.953 1 2 ? N5 MTX 200 A 1 HETATM 9 C C6 MTX . . . D 3 18.832 58.81 24.035 1 2 ? C6 MTX 200 A 1 HETATM 10 C C7 MTX . . . D 3 19.624 59.222 25.087 1 2 ? C7 MTX 200 A 1 HETATM 11 N N8 MTX . . . D 3 20.989 59.216 25.168 1 2 ? N8 MTX 200 A 1 HETATM 12 C C8A MTX . . . D 3 21.52 58.725 24.024 1 2 ? C8A MTX 200 A 1 HETATM 13 C C9 MTX . . . D 3 17.324 58.85 24.129 1 2.6 ? C9 MTX 200 A 1 HETATM 14 N N10 MTX . . . D 3 16.844 59.972 25.116 1 2 ? N10 MTX 200 A 1 HETATM 15 C CM MTX . . . D 3 15.952 59.09 25.992 1 2 ? CM MTX 200 A 1 HETATM 16 C C11 MTX . . . D 3 17.795 64.082 25.394 1 4.66 ? C11 MTX 200 A 1 HETATM 17 C C12 MTX . . . D 3 17.184 63.343 26.412 1 2 ? C12 MTX 200 A 1 HETATM 18 C C13 MTX . . . D 3 16.924 62.006 26.256 1 3 ? C13 MTX 200 A 1 HETATM 19 C C14 MTX . . . D 3 17.265 61.341 25.077 1 4.1 ? C14 MTX 200 A 1 HETATM 20 C C15 MTX . . . D 3 17.894 62.074 24.063 1 2 ? C15 MTX 200 A 1 HETATM 21 C C16 MTX . . . D 3 18.154 63.411 24.22 1 3.8 ? C16 MTX 200 A 1 HETATM 22 C C MTX . . . D 3 17.843 65.559 25.69 1 5.83 ? C MTX 200 A 1 HETATM 23 O O MTX . . . D 3 17.255 66.066 26.66 1 6.68 ? O MTX 200 A 1 HETATM 24 N N MTX . . . D 3 18.43 66.303 24.764 1 5.89 ? N MTX 200 A 1 HETATM 25 C CA MTX . . . D 3 19.861 66.28 24.514 1 6.44 ? CA MTX 200 A 1 HETATM 26 C CT MTX . . . D 3 20.05 66.946 23.182 1 5.4 ? CT MTX 200 A 1 HETATM 27 O O1 MTX . . . D 3 20.343 66.19 22.231 1 6.03 ? O1 MTX 200 A 1 HETATM 28 O O2 MTX . . . D 3 19.795 68.168 23.102 1 6.61 ? O2 MTX 200 A 1 HETATM 29 C CB MTX . . . D 3 20.631 67.024 25.618 1 5.79 ? CB MTX 200 A 1 HETATM 30 C CG MTX . . . D 3 19.984 68.317 26.085 1 3.8 ? CG MTX 200 A 1 HETATM 31 C CD MTX . . . D 3 20.58 68.848 27.365 1 2 ? CD MTX 200 A 1 HETATM 32 O OE1 MTX . . . D 3 21.436 68.154 27.961 1 2 ? OE1 MTX 200 A 1 HETATM 33 O OE2 MTX . . . D 3 20.196 69.972 27.77 1 2 ? OE2 MTX 200 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #