data_2DMR # _model_server_result.job_id dBcct_C8vKG0Xr7aVnwSTA _model_server_result.datetime_utc '2024-10-14 08:24:04' _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 2dmr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":783}' # _entry.id 2DMR # _exptl.entry_id 2DMR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 738.541 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE' _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 90 _cell.entry_id 2DMR _cell.length_a 81.03 _cell.length_b 81.03 _cell.length_c 230.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DMR _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 OG SER 189 A SER 147 1_555 D MO 4MO . A 4MO 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc2 B S12 PGD . A PGD 782 1_555 D MO 4MO . A 4MO 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 B S13 PGD . A PGD 782 1_555 D MO 4MO . A 4MO 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc4 C S12 PGD . A PGD 783 1_555 D MO 4MO . A 4MO 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc5 C S13 PGD . A PGD 783 1_555 D MO 4MO . A 4MO 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc6 D MO 4MO . A 4MO 784 1_555 E O O . A O 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? hydrog ? hydrog1 A NE1 TRP 158 A TRP 116 1_555 E O O . A O 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C20 H24 N10 O13 P2 S2' _chem_comp.formula_weight 738.541 _chem_comp.id PGD _chem_comp.mon_nstd_flag . _chem_comp.name '2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE' _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 PB O1B PGD doub 237 n n PB O2B PGD sing 238 n n PB O3B PGD sing 239 n n PB O5' PGD sing 240 n n O2B HOB2 PGD sing 241 n n O3B PA PGD sing 242 n n O3A PA PGD sing 243 n n O3A C10 PGD sing 244 n n PA O1A PGD doub 245 n n PA O2A PGD sing 246 n n O2A HOA2 PGD sing 247 n n O5' C5' PGD sing 248 n n C5' C4' PGD sing 249 n n C5' "H5'1" PGD sing 250 n n C5' "H5'2" PGD sing 251 n n C4' O4' PGD sing 252 n n C4' C3' PGD sing 253 n n C4' H4' PGD sing 254 n n O4' C1' PGD sing 255 n n C3' O3' PGD sing 256 n n C3' C2' PGD sing 257 n n C3' H3' PGD sing 258 n n O3' HO3' PGD sing 259 n n C2' O2' PGD sing 260 n n C2' C1' PGD sing 261 n n C2' H2' PGD sing 262 n n O2' HO2' PGD sing 263 n n C1' N9 PGD sing 264 n n C1' H1' PGD sing 265 n n N9 C8 PGD sing 266 n y N9 C4 PGD sing 267 n y C8 N7 PGD doub 268 n y C8 H8 PGD sing 269 n n N7 C5 PGD sing 270 n y C5 C6 PGD sing 271 n n C5 C4 PGD doub 272 n y C6 O6 PGD doub 273 n n C6 N1 PGD sing 274 n n N1 C2 PGD sing 275 n n N1 HN1 PGD sing 276 n n C2 N2 PGD sing 277 n n C2 N3 PGD doub 278 n n N2 HN21 PGD sing 279 n n N2 HN22 PGD sing 280 n n N3 C4 PGD sing 281 n n C10 C11 PGD sing 282 n n C10 H101 PGD sing 283 n n C10 H102 PGD sing 284 n n C11 O11 PGD sing 285 n n C11 C12 PGD sing 286 n n C11 H11 PGD sing 287 n n O11 C23 PGD sing 288 n n C12 S12 PGD sing 289 n n C12 C13 PGD doub 290 n n S12 H12 PGD sing 291 n n C13 S13 PGD sing 292 n n C13 C14 PGD sing 293 n n S13 H13 PGD sing 294 n n C14 N15 PGD sing 295 n n C14 C23 PGD sing 296 n n C14 H14 PGD sing 297 n n N15 C16 PGD doub 298 n n C16 C17 PGD sing 299 n n C16 C21 PGD sing 300 n n C17 O17 PGD doub 301 n n C17 N18 PGD sing 302 n n N18 C19 PGD doub 303 n n C19 N19 PGD sing 304 n n C19 N20 PGD sing 305 n n N19 H191 PGD sing 306 n n N19 H192 PGD sing 307 n n N20 C21 PGD doub 308 n n C21 N22 PGD sing 309 n n N22 C23 PGD sing 310 n n N22 H22 PGD sing 311 n n C23 H23 PGD sing 312 n n # _atom_sites.entry_id 2DMR _atom_sites.fract_transf_matrix[1][1] 0.012341 _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] 0.012341 _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] 0.004347 _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 B 2 PGD A 1 782 1 PGD PGD . C 2 PGD A 1 783 2 PGD PGD . D 3 4MO A 1 784 3 4MO 4MO . E 4 O A 1 785 4 O O . F 5 SO2 A 1 786 1 SO2 SO2 . G 6 HOH A 1 787 2 HOH HOH . G 6 HOH A 2 788 3 HOH HOH . G 6 HOH A 3 789 4 HOH HOH . G 6 HOH A 4 790 5 HOH HOH . G 6 HOH A 5 791 6 HOH HOH . G 6 HOH A 6 792 7 HOH HOH . G 6 HOH A 7 793 8 HOH HOH . G 6 HOH A 8 794 9 HOH HOH . G 6 HOH A 9 795 10 HOH HOH . G 6 HOH A 10 796 11 HOH HOH . G 6 HOH A 11 797 12 HOH HOH . G 6 HOH A 12 798 13 HOH HOH . G 6 HOH A 13 799 14 HOH HOH . G 6 HOH A 14 800 15 HOH HOH . G 6 HOH A 15 801 16 HOH HOH . G 6 HOH A 16 802 17 HOH HOH . G 6 HOH A 17 803 18 HOH HOH . G 6 HOH A 18 804 19 HOH HOH . G 6 HOH A 19 805 20 HOH HOH . G 6 HOH A 20 806 21 HOH HOH . G 6 HOH A 21 807 22 HOH HOH . G 6 HOH A 22 808 23 HOH HOH . G 6 HOH A 23 809 24 HOH HOH . G 6 HOH A 24 810 25 HOH HOH . G 6 HOH A 25 811 26 HOH HOH . G 6 HOH A 26 812 27 HOH HOH . G 6 HOH A 27 813 28 HOH HOH . G 6 HOH A 28 814 29 HOH HOH . G 6 HOH A 29 815 30 HOH HOH . G 6 HOH A 30 816 31 HOH HOH . G 6 HOH A 31 817 32 HOH HOH . G 6 HOH A 32 818 33 HOH HOH . G 6 HOH A 33 819 34 HOH HOH . G 6 HOH A 34 820 35 HOH HOH . G 6 HOH A 35 821 36 HOH HOH . G 6 HOH A 36 822 37 HOH HOH . G 6 HOH A 37 823 38 HOH HOH . G 6 HOH A 38 824 39 HOH HOH . G 6 HOH A 39 825 40 HOH HOH . G 6 HOH A 40 826 41 HOH HOH . G 6 HOH A 41 827 42 HOH HOH . G 6 HOH A 42 828 43 HOH HOH . G 6 HOH A 43 829 44 HOH HOH . G 6 HOH A 44 830 45 HOH HOH . G 6 HOH A 45 831 46 HOH HOH . G 6 HOH A 46 832 47 HOH HOH . G 6 HOH A 47 833 48 HOH HOH . G 6 HOH A 48 834 49 HOH HOH . G 6 HOH A 49 835 50 HOH HOH . G 6 HOH A 50 836 51 HOH HOH . G 6 HOH A 51 837 52 HOH HOH . G 6 HOH A 52 838 53 HOH HOH . G 6 HOH A 53 839 54 HOH HOH . G 6 HOH A 54 840 55 HOH HOH . G 6 HOH A 55 841 56 HOH HOH . G 6 HOH A 56 842 57 HOH HOH . G 6 HOH A 57 843 58 HOH HOH . G 6 HOH A 58 844 59 HOH HOH . G 6 HOH A 59 845 60 HOH HOH . G 6 HOH A 60 846 61 HOH HOH . G 6 HOH A 61 847 62 HOH HOH . G 6 HOH A 62 848 63 HOH HOH . G 6 HOH A 63 849 64 HOH HOH . G 6 HOH A 64 850 65 HOH HOH . G 6 HOH A 65 851 66 HOH HOH . G 6 HOH A 66 852 67 HOH HOH . G 6 HOH A 67 853 68 HOH HOH . G 6 HOH A 68 854 69 HOH HOH . G 6 HOH A 69 855 70 HOH HOH . G 6 HOH A 70 856 71 HOH HOH . G 6 HOH A 71 857 72 HOH HOH . G 6 HOH A 72 858 73 HOH HOH . G 6 HOH A 73 859 74 HOH HOH . G 6 HOH A 74 860 75 HOH HOH . G 6 HOH A 75 861 76 HOH HOH . G 6 HOH A 76 862 77 HOH HOH . G 6 HOH A 77 863 78 HOH HOH . G 6 HOH A 78 864 79 HOH HOH . G 6 HOH A 79 865 80 HOH HOH . G 6 HOH A 80 866 81 HOH HOH . G 6 HOH A 81 867 82 HOH HOH . G 6 HOH A 82 868 83 HOH HOH . G 6 HOH A 83 869 84 HOH HOH . G 6 HOH A 84 870 85 HOH HOH . G 6 HOH A 85 871 86 HOH HOH . G 6 HOH A 86 872 87 HOH HOH . G 6 HOH A 87 873 88 HOH HOH . G 6 HOH A 88 874 89 HOH HOH . G 6 HOH A 89 875 90 HOH HOH . G 6 HOH A 90 876 91 HOH HOH . G 6 HOH A 91 877 92 HOH HOH . G 6 HOH A 92 878 93 HOH HOH . G 6 HOH A 93 879 94 HOH HOH . G 6 HOH A 94 880 95 HOH HOH . G 6 HOH A 95 881 96 HOH HOH . G 6 HOH A 96 882 97 HOH HOH . G 6 HOH A 97 883 98 HOH HOH . G 6 HOH A 98 884 99 HOH HOH . G 6 HOH A 99 885 100 HOH HOH . G 6 HOH A 100 886 101 HOH HOH . G 6 HOH A 101 887 102 HOH HOH . G 6 HOH A 102 888 103 HOH HOH . G 6 HOH A 103 889 104 HOH HOH . G 6 HOH A 104 890 105 HOH HOH . G 6 HOH A 105 891 106 HOH HOH . G 6 HOH A 106 892 107 HOH HOH . G 6 HOH A 107 893 108 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 P PB PGD . . . C 2 -9.089 54.198 36.026 1 12.06 ? PB PGD 783 A 1 HETATM 2 O O1B PGD . . . C 2 -8.104 53.136 36.97 1 13.34 ? O1B PGD 783 A 1 HETATM 3 O O2B PGD . . . C 2 -8.167 55.534 35.466 1 13.46 ? O2B PGD 783 A 1 HETATM 4 O O3B PGD . . . C 2 -9.636 53.376 34.784 1 12.76 ? O3B PGD 783 A 1 HETATM 5 O O3A PGD . . . C 2 -9.854 51.8 32.615 1 14.31 ? O3A PGD 783 A 1 HETATM 6 P PA PGD . . . C 2 -10.252 51.983 34.288 1 11.94 ? PA PGD 783 A 1 HETATM 7 O O1A PGD . . . C 2 -11.956 52.041 34.565 1 13.93 ? O1A PGD 783 A 1 HETATM 8 O O2A PGD . . . C 2 -9.573 50.746 35.27 1 14.72 ? O2A PGD 783 A 1 HETATM 9 O O5' PGD . . . C 2 -10.419 54.758 36.955 1 13.93 ? O5' PGD 783 A 1 HETATM 10 C C5' PGD . . . C 2 -11.332 55.395 36.12 1 13.44 ? C5' PGD 783 A 1 HETATM 11 C C4' PGD . . . C 2 -11.995 56.424 37.043 1 13.65 ? C4' PGD 783 A 1 HETATM 12 O O4' PGD . . . C 2 -12.388 55.755 38.214 1 14.02 ? O4' PGD 783 A 1 HETATM 13 C C3' PGD . . . C 2 -10.944 57.447 37.432 1 14.04 ? C3' PGD 783 A 1 HETATM 14 O O3' PGD . . . C 2 -11.332 58.683 36.92 1 13.77 ? O3' PGD 783 A 1 HETATM 15 C C2' PGD . . . C 2 -10.884 57.377 38.93 1 14.7 ? C2' PGD 783 A 1 HETATM 16 O O2' PGD . . . C 2 -10.73 58.597 39.579 1 14.26 ? O2' PGD 783 A 1 HETATM 17 C C1' PGD . . . C 2 -12.214 56.71 39.239 1 14.34 ? C1' PGD 783 A 1 HETATM 18 N N9 PGD . . . C 2 -12.319 56.121 40.554 1 13.85 ? N9 PGD 783 A 1 HETATM 19 C C8 PGD . . . C 2 -11.293 55.755 41.373 1 13.51 ? C8 PGD 783 A 1 HETATM 20 N N7 PGD . . . C 2 -11.724 55.24 42.547 1 12.93 ? N7 PGD 783 A 1 HETATM 21 C C5 PGD . . . C 2 -13.065 55.379 42.491 1 13.61 ? C5 PGD 783 A 1 HETATM 22 C C6 PGD . . . C 2 -14.052 54.74 43.238 1 13.18 ? C6 PGD 783 A 1 HETATM 23 O O6 PGD . . . C 2 -13.827 54.112 44.25 1 12.51 ? O6 PGD 783 A 1 HETATM 24 N N1 PGD . . . C 2 -15.363 55.065 42.989 1 13.4 ? N1 PGD 783 A 1 HETATM 25 C C2 PGD . . . C 2 -15.673 55.858 41.908 1 13.37 ? C2 PGD 783 A 1 HETATM 26 N N2 PGD . . . C 2 -17.052 56.082 41.651 1 12.87 ? N2 PGD 783 A 1 HETATM 27 N N3 PGD . . . C 2 -14.709 56.148 40.98 1 13.33 ? N3 PGD 783 A 1 HETATM 28 C C4 PGD . . . C 2 -13.41 55.935 41.299 1 13.69 ? C4 PGD 783 A 1 HETATM 29 C C10 PGD . . . C 2 -8.799 50.894 32.583 1 14.66 ? C10 PGD 783 A 1 HETATM 30 C C11 PGD . . . C 2 -8.301 50.658 31.167 1 14.42 ? C11 PGD 783 A 1 HETATM 31 O O11 PGD . . . C 2 -7.91 51.863 30.57 1 13.65 ? O11 PGD 783 A 1 HETATM 32 C C12 PGD . . . C 2 -7.232 49.618 31.197 1 15.21 ? C12 PGD 783 A 1 HETATM 33 S S12 PGD . . . C 2 -7.263 48.032 32.08 1 18.78 ? S12 PGD 783 A 1 HETATM 34 C C13 PGD . . . C 2 -6.02 49.801 30.587 1 14.62 ? C13 PGD 783 A 1 HETATM 35 S S13 PGD . . . C 2 -5.069 48.263 30.652 1 15.87 ? S13 PGD 783 A 1 HETATM 36 C C14 PGD . . . C 2 -5.742 51.009 29.786 1 13.37 ? C14 PGD 783 A 1 HETATM 37 N N15 PGD . . . C 2 -4.857 51.953 30.469 1 12.29 ? N15 PGD 783 A 1 HETATM 38 C C16 PGD . . . C 2 -4.658 53.259 29.934 1 12.25 ? C16 PGD 783 A 1 HETATM 39 C C17 PGD . . . C 2 -3.619 54.121 30.288 1 12.77 ? C17 PGD 783 A 1 HETATM 40 O O17 PGD . . . C 2 -2.652 53.8 30.968 1 13.49 ? O17 PGD 783 A 1 HETATM 41 N N18 PGD . . . C 2 -3.527 55.369 29.745 1 11.96 ? N18 PGD 783 A 1 HETATM 42 C C19 PGD . . . C 2 -4.5 55.819 28.921 1 11.55 ? C19 PGD 783 A 1 HETATM 43 N N19 PGD . . . C 2 -4.615 57.216 28.734 1 11.5 ? N19 PGD 783 A 1 HETATM 44 N N20 PGD . . . C 2 -5.54 55.01 28.604 1 12.29 ? N20 PGD 783 A 1 HETATM 45 C C21 PGD . . . C 2 -5.644 53.733 29.066 1 12.13 ? C21 PGD 783 A 1 HETATM 46 N N22 PGD . . . C 2 -6.811 52.961 28.783 1 11.12 ? N22 PGD 783 A 1 HETATM 47 C C23 PGD . . . C 2 -7.088 51.707 29.463 1 12.81 ? C23 PGD 783 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 47 #