data_3IIF # _model_server_result.job_id rEuHdwP5DIAdF8EAhgD5fA _model_server_result.datetime_utc '2024-12-09 23:27:32' _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 3iif # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":400}' # _entry.id 3IIF # _exptl.entry_id 3IIF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _entity.pdbx_number_of_molecules 3 _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 3IIF _cell.length_a 129.61 _cell.length_b 129.61 _cell.length_c 128.29 _cell.Z_PDB 27 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IIF _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 3IIF _atom_sites.fract_transf_matrix[1][1] 0.007715 _atom_sites.fract_transf_matrix[1][2] 0.004455 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008909 _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] 0.007795 _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 D 2 APR A 1 400 400 APR APR . E 2 APR B 1 400 400 APR APR . F 2 APR C 1 400 400 APR APR . G 3 HOH A 1 4 4 HOH HOH . G 3 HOH A 2 6 6 HOH HOH . G 3 HOH A 3 7 7 HOH HOH . G 3 HOH A 4 8 8 HOH HOH . G 3 HOH A 5 9 9 HOH HOH . G 3 HOH A 6 10 10 HOH HOH . G 3 HOH A 7 12 12 HOH HOH . G 3 HOH A 8 15 15 HOH HOH . G 3 HOH A 9 16 16 HOH HOH . G 3 HOH A 10 17 17 HOH HOH . G 3 HOH A 11 18 18 HOH HOH . G 3 HOH A 12 21 21 HOH HOH . G 3 HOH A 13 23 23 HOH HOH . G 3 HOH A 14 27 27 HOH HOH . G 3 HOH A 15 28 28 HOH HOH . G 3 HOH A 16 29 29 HOH HOH . G 3 HOH A 17 31 31 HOH HOH . G 3 HOH A 18 34 34 HOH HOH . G 3 HOH A 19 37 37 HOH HOH . G 3 HOH A 20 39 39 HOH HOH . G 3 HOH A 21 49 49 HOH HOH . G 3 HOH A 22 50 50 HOH HOH . G 3 HOH A 23 54 54 HOH HOH . G 3 HOH A 24 55 55 HOH HOH . G 3 HOH A 25 60 60 HOH HOH . G 3 HOH A 26 61 61 HOH HOH . G 3 HOH A 27 65 65 HOH HOH . G 3 HOH A 28 68 68 HOH HOH . G 3 HOH A 29 70 70 HOH HOH . G 3 HOH A 30 74 74 HOH HOH . G 3 HOH A 31 79 79 HOH HOH . G 3 HOH A 32 81 81 HOH HOH . G 3 HOH A 33 86 86 HOH HOH . G 3 HOH A 34 90 90 HOH HOH . G 3 HOH A 35 96 96 HOH HOH . G 3 HOH A 36 97 97 HOH HOH . G 3 HOH A 37 100 100 HOH HOH . G 3 HOH A 38 101 101 HOH HOH . G 3 HOH A 39 102 102 HOH HOH . G 3 HOH A 40 105 105 HOH HOH . G 3 HOH A 41 106 106 HOH HOH . G 3 HOH A 42 111 111 HOH HOH . G 3 HOH A 43 112 112 HOH HOH . G 3 HOH A 44 113 113 HOH HOH . G 3 HOH A 45 116 116 HOH HOH . G 3 HOH A 46 117 117 HOH HOH . G 3 HOH A 47 118 118 HOH HOH . G 3 HOH A 48 121 121 HOH HOH . G 3 HOH A 49 125 125 HOH HOH . G 3 HOH A 50 126 126 HOH HOH . G 3 HOH A 51 130 130 HOH HOH . G 3 HOH A 52 131 131 HOH HOH . G 3 HOH A 53 135 135 HOH HOH . G 3 HOH A 54 137 137 HOH HOH . G 3 HOH A 55 142 142 HOH HOH . G 3 HOH A 56 144 144 HOH HOH . G 3 HOH A 57 148 148 HOH HOH . G 3 HOH A 58 150 150 HOH HOH . G 3 HOH A 59 151 151 HOH HOH . G 3 HOH A 60 152 152 HOH HOH . G 3 HOH A 61 153 153 HOH HOH . G 3 HOH A 62 156 156 HOH HOH . G 3 HOH A 63 157 157 HOH HOH . G 3 HOH A 64 158 158 HOH HOH . G 3 HOH A 65 370 161 HOH HOH . G 3 HOH A 66 371 163 HOH HOH . G 3 HOH A 67 372 166 HOH HOH . H 3 HOH B 1 1 1 HOH HOH . H 3 HOH B 2 11 11 HOH HOH . H 3 HOH B 3 13 13 HOH HOH . H 3 HOH B 4 14 14 HOH HOH . H 3 HOH B 5 19 19 HOH HOH . H 3 HOH B 6 25 25 HOH HOH . H 3 HOH B 7 26 26 HOH HOH . H 3 HOH B 8 30 30 HOH HOH . H 3 HOH B 9 35 35 HOH HOH . H 3 HOH B 10 36 36 HOH HOH . H 3 HOH B 11 38 38 HOH HOH . H 3 HOH B 12 40 40 HOH HOH . H 3 HOH B 13 41 41 HOH HOH . H 3 HOH B 14 43 43 HOH HOH . H 3 HOH B 15 44 44 HOH HOH . H 3 HOH B 16 47 47 HOH HOH . H 3 HOH B 17 48 48 HOH HOH . H 3 HOH B 18 51 51 HOH HOH . H 3 HOH B 19 52 52 HOH HOH . H 3 HOH B 20 53 53 HOH HOH . H 3 HOH B 21 56 56 HOH HOH . H 3 HOH B 22 57 57 HOH HOH . H 3 HOH B 23 58 58 HOH HOH . H 3 HOH B 24 62 62 HOH HOH . H 3 HOH B 25 67 67 HOH HOH . H 3 HOH B 26 69 69 HOH HOH . H 3 HOH B 27 71 71 HOH HOH . H 3 HOH B 28 73 73 HOH HOH . H 3 HOH B 29 75 75 HOH HOH . H 3 HOH B 30 76 76 HOH HOH . H 3 HOH B 31 78 78 HOH HOH . H 3 HOH B 32 83 83 HOH HOH . H 3 HOH B 33 85 85 HOH HOH . H 3 HOH B 34 88 88 HOH HOH . H 3 HOH B 35 91 91 HOH HOH . H 3 HOH B 36 92 92 HOH HOH . H 3 HOH B 37 93 93 HOH HOH . H 3 HOH B 38 98 98 HOH HOH . H 3 HOH B 39 103 103 HOH HOH . H 3 HOH B 40 107 107 HOH HOH . H 3 HOH B 41 108 108 HOH HOH . H 3 HOH B 42 114 114 HOH HOH . H 3 HOH B 43 115 115 HOH HOH . H 3 HOH B 44 122 122 HOH HOH . H 3 HOH B 45 124 124 HOH HOH . H 3 HOH B 46 127 127 HOH HOH . H 3 HOH B 47 132 132 HOH HOH . H 3 HOH B 48 133 133 HOH HOH . H 3 HOH B 49 134 134 HOH HOH . H 3 HOH B 50 136 136 HOH HOH . H 3 HOH B 51 138 138 HOH HOH . H 3 HOH B 52 139 139 HOH HOH . H 3 HOH B 53 143 143 HOH HOH . H 3 HOH B 54 145 145 HOH HOH . H 3 HOH B 55 146 146 HOH HOH . H 3 HOH B 56 147 147 HOH HOH . H 3 HOH B 57 154 154 HOH HOH . H 3 HOH B 58 155 155 HOH HOH . H 3 HOH B 59 370 160 HOH HOH . H 3 HOH B 60 371 162 HOH HOH . H 3 HOH B 61 372 164 HOH HOH . H 3 HOH B 62 373 165 HOH HOH . H 3 HOH B 63 374 167 HOH HOH . I 3 HOH C 1 2 2 HOH HOH . I 3 HOH C 2 3 3 HOH HOH . I 3 HOH C 3 5 5 HOH HOH . I 3 HOH C 4 20 20 HOH HOH . I 3 HOH C 5 22 22 HOH HOH . I 3 HOH C 6 24 24 HOH HOH . I 3 HOH C 7 32 32 HOH HOH . I 3 HOH C 8 33 33 HOH HOH . I 3 HOH C 9 42 42 HOH HOH . I 3 HOH C 10 45 45 HOH HOH . I 3 HOH C 11 46 46 HOH HOH . I 3 HOH C 12 59 59 HOH HOH . I 3 HOH C 13 63 63 HOH HOH . I 3 HOH C 14 64 64 HOH HOH . I 3 HOH C 15 66 66 HOH HOH . I 3 HOH C 16 72 72 HOH HOH . I 3 HOH C 17 77 77 HOH HOH . I 3 HOH C 18 80 80 HOH HOH . I 3 HOH C 19 82 82 HOH HOH . I 3 HOH C 20 84 84 HOH HOH . I 3 HOH C 21 87 87 HOH HOH . I 3 HOH C 22 89 89 HOH HOH . I 3 HOH C 23 94 94 HOH HOH . I 3 HOH C 24 95 95 HOH HOH . I 3 HOH C 25 99 99 HOH HOH . I 3 HOH C 26 104 104 HOH HOH . I 3 HOH C 27 109 109 HOH HOH . I 3 HOH C 28 110 110 HOH HOH . I 3 HOH C 29 119 119 HOH HOH . I 3 HOH C 30 120 120 HOH HOH . I 3 HOH C 31 123 123 HOH HOH . I 3 HOH C 32 128 128 HOH HOH . I 3 HOH C 33 129 129 HOH HOH . I 3 HOH C 34 140 140 HOH HOH . I 3 HOH C 35 141 141 HOH HOH . I 3 HOH C 36 149 149 HOH HOH . I 3 HOH C 37 370 159 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 APR . . . F 2 22.08 5.501 24.398 1 28.76 ? N1 APR 400 C 1 HETATM 2 C C2 APR . . . F 2 21.608 4.828 23.318 1 28 ? C2 APR 400 C 1 HETATM 3 N N3 APR . . . F 2 20.356 4.365 23.232 1 26.88 ? N3 APR 400 C 1 HETATM 4 C C4 APR . . . F 2 19.476 4.588 24.255 1 28.22 ? C4 APR 400 C 1 HETATM 5 C C5 APR . . . F 2 19.898 5.319 25.446 1 28.06 ? C5 APR 400 C 1 HETATM 6 C C6 APR . . . F 2 21.29 5.762 25.457 1 27.86 ? C6 APR 400 C 1 HETATM 7 N N6 APR . . . F 2 21.723 6.407 26.521 1 28.54 ? N6 APR 400 C 1 HETATM 8 N N7 APR . . . F 2 18.869 5.356 26.303 1 28.3 ? N7 APR 400 C 1 HETATM 9 C C8 APR . . . F 2 17.826 4.745 25.707 1 27.52 ? C8 APR 400 C 1 HETATM 10 N N9 APR . . . F 2 18.207 4.281 24.496 1 27.2 ? N9 APR 400 C 1 HETATM 11 C C1' APR . . . F 2 17.424 3.579 23.51 1 27.46 ? C1' APR 400 C 1 HETATM 12 C C2' APR . . . F 2 16.027 3.113 23.95 1 27.41 ? C2' APR 400 C 1 HETATM 13 O O2' APR . . . F 2 16.077 1.931 24.7 1 24.88 ? O2' APR 400 C 1 HETATM 14 C C3' APR . . . F 2 15.336 2.928 22.621 1 27.01 ? C3' APR 400 C 1 HETATM 15 O O3' APR . . . F 2 15.544 1.57 22.175 1 26.95 ? O3' APR 400 C 1 HETATM 16 O O4' APR . . . F 2 17.134 4.522 22.501 1 27.08 ? O4' APR 400 C 1 HETATM 17 C C4' APR . . . F 2 16.013 3.997 21.743 1 27.94 ? C4' APR 400 C 1 HETATM 18 C C5' APR . . . F 2 15.093 5.118 21.24 1 29.25 ? C5' APR 400 C 1 HETATM 19 O O5' APR . . . F 2 14.251 5.639 22.28 1 30.35 ? O5' APR 400 C 1 HETATM 20 P PA APR . . . F 2 13.773 7.163 22.281 1 28.8 ? PA APR 400 C 1 HETATM 21 O O1A APR . . . F 2 14.957 8.071 22.446 1 29.14 ? O1A APR 400 C 1 HETATM 22 O O2A APR . . . F 2 12.598 7.247 23.243 1 31.04 ? O2A APR 400 C 1 HETATM 23 O O3A APR . . . F 2 13.322 7.467 20.773 1 28.54 ? O3A APR 400 C 1 HETATM 24 P PB APR . . . F 2 11.956 7.156 19.977 1 30.19 ? PB APR 400 C 1 HETATM 25 O O1B APR . . . F 2 12.285 7.367 18.521 1 25.87 ? O1B APR 400 C 1 HETATM 26 O O2B APR . . . F 2 11.356 5.861 20.43 1 29.92 ? O2B APR 400 C 1 HETATM 27 O O5D APR . . . F 2 10.925 8.372 20.274 1 36.15 ? O5D APR 400 C 1 HETATM 28 C C5D APR . . . F 2 11.366 9.628 20.771 1 44.23 ? C5D APR 400 C 1 HETATM 29 O O4D APR . . . F 2 10.879 11.968 20.915 1 53.65 ? O4D APR 400 C 1 HETATM 30 O O1D APR . . . F 2 10.145 13.89 21.904 1 55.71 ? O1D APR 400 C 1 HETATM 31 C C1D APR . . . F 2 9.801 12.902 20.943 1 55.3 ? C1D APR 400 C 1 HETATM 32 O O2D APR . . . F 2 7.531 12.135 20.365 1 57.99 ? O2D APR 400 C 1 HETATM 33 C C2D APR . . . F 2 8.563 12.111 21.351 1 55.75 ? C2D APR 400 C 1 HETATM 34 O O3D APR . . . F 2 9.489 10.614 22.871 1 57.85 ? O3D APR 400 C 1 HETATM 35 C C3D APR . . . F 2 9.094 10.707 21.506 1 54.22 ? C3D APR 400 C 1 HETATM 36 C C4D APR . . . F 2 10.304 10.706 20.595 1 50.65 ? C4D APR 400 C 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #