data_1FDI # _model_server_result.job_id bJ4rKqgwMVjJPAITCbK1Tg _model_server_result.datetime_utc '2024-11-26 07:23:53' _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 1fdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":802}' # _entry.id 1FDI # _exptl.entry_id 1FDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 740.557 _entity.id 4 _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 1FDI _cell.length_a 146.8 _cell.length_b 146.8 _cell.length_c 81.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FDI _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 ? 4 D N N ? 4 E 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 SG CYS 8 A CYS 8 1_555 C FE2 SF4 . A SF4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 A SG CYS 11 A CYS 11 1_555 C FE4 SF4 . A SF4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 A SG CYS 15 A CYS 15 1_555 C FE3 SF4 . A SF4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc4 A SG CYS 42 A CYS 42 1_555 C FE1 SF4 . A SF4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A SE SEC 140 A SEC 140 1_555 F MO 6MO . A 6MO 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc6 D S12 MGD . A MGD 801 1_555 F MO 6MO . A 6MO 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc7 D S13 MGD . A MGD 801 1_555 F MO 6MO . A 6MO 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc8 E S12 MGD . A MGD 802 1_555 F MO 6MO . A 6MO 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc9 E S13 MGD . A MGD 802 1_555 F MO 6MO . A 6MO 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc10 F MO 6MO . A 6MO 803 1_555 B O1 NO2 . A NO2 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? # _chem_comp.formula 'C20 H26 N10 O13 P2 S2' _chem_comp.formula_weight 740.557 _chem_comp.id MGD _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 'MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE' # 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 MGD doub 237 n n PB O2B MGD sing 238 n n PB O3B MGD sing 239 n n PB O5' MGD sing 240 n n O2B HOB2 MGD sing 241 n n O3B PA MGD sing 242 n n O3A PA MGD sing 243 n n O3A C10 MGD sing 244 n n PA O1A MGD doub 245 n n PA O2A MGD sing 246 n n O2A HOA2 MGD sing 247 n n O5' C5' MGD sing 248 n n C5' C4' MGD sing 249 n n C5' "H5'1" MGD sing 250 n n C5' "H5'2" MGD sing 251 n n C4' O4' MGD sing 252 n n C4' C3' MGD sing 253 n n C4' H4' MGD sing 254 n n O4' C1' MGD sing 255 n n C3' O3' MGD sing 256 n n C3' C2' MGD sing 257 n n C3' H3' MGD sing 258 n n O3' HO3' MGD sing 259 n n C2' O2' MGD sing 260 n n C2' C1' MGD sing 261 n n C2' H2' MGD sing 262 n n O2' HO2' MGD sing 263 n n C1' N9 MGD sing 264 n n C1' H1' MGD sing 265 n n N9 C8 MGD sing 266 n y N9 C4 MGD sing 267 n y C8 N7 MGD doub 268 n y C8 H8 MGD sing 269 n n N7 C5 MGD sing 270 n y C5 C6 MGD sing 271 n n C5 C4 MGD doub 272 n y C6 O6 MGD doub 273 n n C6 N1 MGD sing 274 n n N1 C2 MGD sing 275 n n N1 HN1 MGD sing 276 n n C2 N2 MGD sing 277 n n C2 N3 MGD doub 278 n n N2 HN21 MGD sing 279 n n N2 HN22 MGD sing 280 n n N3 C4 MGD sing 281 n n C10 C11 MGD sing 282 n n C10 H101 MGD sing 283 n n C10 H102 MGD sing 284 n n C11 O11 MGD sing 285 n n C11 C12 MGD sing 286 n n C11 H11 MGD sing 287 n n O11 C23 MGD sing 288 n n C12 S12 MGD sing 289 n n C12 C13 MGD doub 290 n n S12 H12 MGD sing 291 n n C13 S13 MGD sing 292 n n C13 C14 MGD sing 293 n n S13 H13 MGD sing 294 n n C14 N15 MGD sing 295 n n C14 C23 MGD sing 296 n n C14 H14 MGD sing 297 n n N15 C16 MGD sing 298 n n N15 H15 MGD sing 299 n n C16 C17 MGD sing 300 n n C16 C21 MGD doub 301 n n C17 O17 MGD doub 302 n n C17 N18 MGD sing 303 n n N18 C19 MGD sing 304 n n N18 H18 MGD sing 305 n n C19 N19 MGD sing 306 n n C19 N20 MGD doub 307 n n N19 H191 MGD sing 308 n n N19 H192 MGD sing 309 n n N20 C21 MGD sing 310 n n C21 N22 MGD sing 311 n n N22 C23 MGD sing 312 n n N22 H22 MGD sing 313 n n C23 H23 MGD sing 314 n n # _atom_sites.entry_id 1FDI _atom_sites.fract_transf_matrix[1][1] 0.006812 _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] 0.006812 _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] 0.012225 _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 NO2 A 1 804 804 NO2 NO2 . C 3 SF4 A 1 800 800 SF4 FS4 . D 4 MGD A 1 801 801 MGD MGD . E 4 MGD A 1 802 802 MGD MGD . F 5 6MO A 1 803 803 6MO 6MO . G 6 HOH A 1 805 1 HOH HOH . G 6 HOH A 2 806 2 HOH HOH . G 6 HOH A 3 807 3 HOH HOH . G 6 HOH A 4 808 4 HOH HOH . G 6 HOH A 5 809 5 HOH HOH . G 6 HOH A 6 810 6 HOH HOH . G 6 HOH A 7 811 7 HOH HOH . G 6 HOH A 8 812 8 HOH HOH . G 6 HOH A 9 813 9 HOH HOH . G 6 HOH A 10 814 11 HOH HOH . G 6 HOH A 11 815 12 HOH HOH . G 6 HOH A 12 816 13 HOH HOH . G 6 HOH A 13 817 14 HOH HOH . G 6 HOH A 14 818 15 HOH HOH . G 6 HOH A 15 819 16 HOH HOH . G 6 HOH A 16 820 17 HOH HOH . G 6 HOH A 17 821 18 HOH HOH . G 6 HOH A 18 822 19 HOH HOH . G 6 HOH A 19 823 20 HOH HOH . G 6 HOH A 20 824 21 HOH HOH . G 6 HOH A 21 825 22 HOH HOH . G 6 HOH A 22 826 23 HOH HOH . G 6 HOH A 23 827 25 HOH HOH . G 6 HOH A 24 828 26 HOH HOH . G 6 HOH A 25 829 27 HOH HOH . G 6 HOH A 26 830 28 HOH HOH . G 6 HOH A 27 831 29 HOH HOH . G 6 HOH A 28 832 30 HOH HOH . G 6 HOH A 29 833 31 HOH HOH . G 6 HOH A 30 834 32 HOH HOH . G 6 HOH A 31 835 33 HOH HOH . G 6 HOH A 32 836 34 HOH HOH . G 6 HOH A 33 837 35 HOH HOH . G 6 HOH A 34 838 36 HOH HOH . G 6 HOH A 35 839 37 HOH HOH . G 6 HOH A 36 840 38 HOH HOH . G 6 HOH A 37 841 39 HOH HOH . G 6 HOH A 38 842 40 HOH HOH . G 6 HOH A 39 843 41 HOH HOH . G 6 HOH A 40 844 42 HOH HOH . G 6 HOH A 41 845 43 HOH HOH . G 6 HOH A 42 846 44 HOH HOH . G 6 HOH A 43 847 47 HOH HOH . G 6 HOH A 44 848 48 HOH HOH . G 6 HOH A 45 849 49 HOH HOH . G 6 HOH A 46 850 50 HOH HOH . G 6 HOH A 47 851 51 HOH HOH . G 6 HOH A 48 852 52 HOH HOH . G 6 HOH A 49 853 53 HOH HOH . G 6 HOH A 50 854 54 HOH HOH . G 6 HOH A 51 855 55 HOH HOH . G 6 HOH A 52 856 56 HOH HOH . G 6 HOH A 53 857 57 HOH HOH . G 6 HOH A 54 858 58 HOH HOH . G 6 HOH A 55 859 59 HOH HOH . G 6 HOH A 56 860 61 HOH HOH . G 6 HOH A 57 861 62 HOH HOH . G 6 HOH A 58 862 65 HOH HOH . G 6 HOH A 59 863 66 HOH HOH . G 6 HOH A 60 864 67 HOH HOH . G 6 HOH A 61 865 70 HOH HOH . G 6 HOH A 62 866 71 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 MGD . . . E 4 76.332 41.776 31.714 1 22.26 ? PB MGD 802 A 1 HETATM 2 O O1B MGD . . . E 4 75.067 41.148 32.088 1 21.33 ? O1B MGD 802 A 1 HETATM 3 O O2B MGD . . . E 4 76.669 41.96 30.28 1 22.29 ? O2B MGD 802 A 1 HETATM 4 O O3B MGD . . . E 4 77.517 40.89 32.333 1 23.56 ? O3B MGD 802 A 1 HETATM 5 O O3A MGD . . . E 4 77.648 38.485 32.706 1 23.38 ? O3A MGD 802 A 1 HETATM 6 P PA MGD . . . E 4 77.709 39.838 33.533 1 25.06 ? PA MGD 802 A 1 HETATM 7 O O1A MGD . . . E 4 79.079 40.11 34.074 1 25.01 ? O1A MGD 802 A 1 HETATM 8 O O2A MGD . . . E 4 76.554 39.896 34.477 1 24.3 ? O2A MGD 802 A 1 HETATM 9 O O5' MGD . . . E 4 76.466 43.178 32.474 1 21.21 ? O5' MGD 802 A 1 HETATM 10 C C5' MGD . . . E 4 76.753 43.223 33.858 1 22.13 ? C5' MGD 802 A 1 HETATM 11 C C4' MGD . . . E 4 76.129 44.421 34.575 1 23.2 ? C4' MGD 802 A 1 HETATM 12 O O4' MGD . . . E 4 76.942 45.567 34.535 1 23.46 ? O4' MGD 802 A 1 HETATM 13 C C3' MGD . . . E 4 74.78 44.808 33.972 1 23.47 ? C3' MGD 802 A 1 HETATM 14 O O3' MGD . . . E 4 73.804 44.658 34.998 1 23.16 ? O3' MGD 802 A 1 HETATM 15 C C2' MGD . . . E 4 74.936 46.286 33.618 1 24.7 ? C2' MGD 802 A 1 HETATM 16 O O2' MGD . . . E 4 73.79 47.057 33.999 1 25.38 ? O2' MGD 802 A 1 HETATM 17 C C1' MGD . . . E 4 76.062 46.679 34.548 1 24.79 ? C1' MGD 802 A 1 HETATM 18 N N9 MGD . . . E 4 76.684 47.966 34.095 1 25.9 ? N9 MGD 802 A 1 HETATM 19 C C8 MGD . . . E 4 76.519 48.666 32.905 1 25.29 ? C8 MGD 802 A 1 HETATM 20 N N7 MGD . . . E 4 77.158 49.809 32.897 1 25.54 ? N7 MGD 802 A 1 HETATM 21 C C5 MGD . . . E 4 77.787 49.868 34.144 1 24.74 ? C5 MGD 802 A 1 HETATM 22 C C6 MGD . . . E 4 78.618 50.856 34.735 1 24.66 ? C6 MGD 802 A 1 HETATM 23 O O6 MGD . . . E 4 78.968 51.885 34.137 1 24.92 ? O6 MGD 802 A 1 HETATM 24 N N1 MGD . . . E 4 79.044 50.563 36.021 1 22.91 ? N1 MGD 802 A 1 HETATM 25 C C2 MGD . . . E 4 78.696 49.407 36.673 1 22.12 ? C2 MGD 802 A 1 HETATM 26 N N2 MGD . . . E 4 79.215 49.164 37.87 1 22.37 ? N2 MGD 802 A 1 HETATM 27 N N3 MGD . . . E 4 77.918 48.498 36.118 1 22.08 ? N3 MGD 802 A 1 HETATM 28 C C4 MGD . . . E 4 77.499 48.761 34.876 1 24.35 ? C4 MGD 802 A 1 HETATM 29 C C10 MGD . . . E 4 78.527 38.26 31.637 1 25.93 ? C10 MGD 802 A 1 HETATM 30 C C11 MGD . . . E 4 78.58 36.782 31.381 1 28.05 ? C11 MGD 802 A 1 HETATM 31 O O11 MGD . . . E 4 77.27 36.271 31.208 1 28.68 ? O11 MGD 802 A 1 HETATM 32 C C12 MGD . . . E 4 79.357 36.45 30.117 1 29.44 ? C12 MGD 802 A 1 HETATM 33 S S12 MGD . . . E 4 80.918 37.239 29.831 1 32.02 ? S12 MGD 802 A 1 HETATM 34 C C13 MGD . . . E 4 78.898 35.413 29.265 1 28.77 ? C13 MGD 802 A 1 HETATM 35 S S13 MGD . . . E 4 79.661 35.166 27.692 1 29.19 ? S13 MGD 802 A 1 HETATM 36 C C14 MGD . . . E 4 77.659 34.599 29.624 1 28.36 ? C14 MGD 802 A 1 HETATM 37 N N15 MGD . . . E 4 76.506 34.943 28.807 1 27.76 ? N15 MGD 802 A 1 HETATM 38 C C16 MGD . . . E 4 75.295 34.516 29.283 1 27.08 ? C16 MGD 802 A 1 HETATM 39 C C17 MGD . . . E 4 74.162 34.46 28.422 1 26.96 ? C17 MGD 802 A 1 HETATM 40 O O17 MGD . . . E 4 74.281 34.589 27.217 1 27.4 ? O17 MGD 802 A 1 HETATM 41 N N18 MGD . . . E 4 72.942 34.11 28.958 1 26.87 ? N18 MGD 802 A 1 HETATM 42 C C19 MGD . . . E 4 72.831 33.814 30.296 1 27.84 ? C19 MGD 802 A 1 HETATM 43 N N19 MGD . . . E 4 71.648 33.808 30.89 1 27.59 ? N19 MGD 802 A 1 HETATM 44 N N20 MGD . . . E 4 73.916 33.817 31.069 1 28.29 ? N20 MGD 802 A 1 HETATM 45 C C21 MGD . . . E 4 75.137 34.173 30.611 1 27.47 ? C21 MGD 802 A 1 HETATM 46 N N22 MGD . . . E 4 76.191 34.165 31.483 1 27.26 ? N22 MGD 802 A 1 HETATM 47 C C23 MGD . . . E 4 77.355 34.878 31.026 1 28.17 ? C23 MGD 802 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 47 #