data_3DYL # _model_server_result.job_id udu54SFWcHzcG94OfBgLWw _model_server_result.datetime_utc '2024-11-26 21:58:16' _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 3dyl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":900}' # _entry.id 3DYL # _exptl.entry_id 3DYL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 222.244 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-ISOBUTYL-1-METHYLXANTHINE _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 90 _cell.entry_id 3DYL _cell.length_a 103.787 _cell.length_b 103.787 _cell.length_c 269.799 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,J 1 1 B,F,G,H,I,K 2 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 5 _struct_asym.id H _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 metalc ? metalc1 A OD2 ASP 116 A ASP 293 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc2 A OD1 ASP 116 A ASP 293 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 A OD1 ASP 225 A ASP 402 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc4 E O1A PCG . A PCG 900 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc5 E O2A PCG . A PCG 900 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc6 C MN MN . A MN 901 1_555 J O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc7 D MG MG . A MG 902 1_555 J O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc8 D MG MG . A MG 902 1_555 J O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc9 D MG MG . A MG 902 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc10 D MG MG . A MG 902 1_555 J O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc11 K O HOH . B HOH 0 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc12 I O1 FMT . B FMT 1 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc13 K O HOH . B HOH 2 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc14 K O HOH . B HOH 3 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc15 K O HOH . B HOH 4 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc16 K O HOH . B HOH 5 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.786 ? metalc ? metalc17 B OD2 ASP 116 B ASP 293 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc18 B OD1 ASP 116 B ASP 293 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc19 B OD1 ASP 225 B ASP 402 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _chem_comp.formula 'C10 H14 N4 O2' _chem_comp.formula_weight 222.244 _chem_comp.id IBM _chem_comp.mon_nstd_flag . _chem_comp.name 3-ISOBUTYL-1-METHYLXANTHINE _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 N9 C8 IBM sing 156 n y N9 C4 IBM sing 157 n y N9 HN9 IBM sing 158 n n C8 N7 IBM doub 159 n y C8 H8 IBM sing 160 n n N7 C5 IBM sing 161 n y C5 C4 IBM doub 162 n y C5 C6 IBM sing 163 n y C4 N3 IBM sing 164 n y N3 C2 IBM sing 165 n y N3 C11 IBM sing 166 n n C2 N1 IBM sing 167 n y C2 O2 IBM doub 168 n n N1 C6 IBM sing 169 n y N1 C10 IBM sing 170 n n C6 O6 IBM doub 171 n n C10 H101 IBM sing 172 n n C10 H102 IBM sing 173 n n C10 H103 IBM sing 174 n n C11 C12 IBM sing 175 n n C11 H111 IBM sing 176 n n C11 H112 IBM sing 177 n n C12 C13 IBM sing 178 n n C12 C14 IBM sing 179 n n C12 H12 IBM sing 180 n n C13 H131 IBM sing 181 n n C13 H132 IBM sing 182 n n C13 H133 IBM sing 183 n n C14 H141 IBM sing 184 n n C14 H142 IBM sing 185 n n C14 H143 IBM sing 186 n n # _atom_sites.entry_id 3DYL _atom_sites.fract_transf_matrix[1][1] 0.009635 _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] 0.009635 _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] 0.003706 _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 MN A 1 901 901 MN MN . D 3 MG A 1 902 902 MG MG . E 4 PCG A 1 900 900 PCG PCG . F 2 MN B 1 901 901 MN MN . G 3 MG B 1 902 902 MG MG . H 5 IBM B 1 900 900 IBM IBM . I 6 FMT B 1 1 1 FMT FMT . J 7 HOH A 1 1 1 HOH HOH . J 7 HOH A 2 2 2 HOH HOH . J 7 HOH A 3 3 3 HOH HOH . J 7 HOH A 4 4 4 HOH HOH . J 7 HOH A 5 5 5 HOH HOH . J 7 HOH A 6 9 9 HOH HOH . J 7 HOH A 7 10 10 HOH HOH . J 7 HOH A 8 12 12 HOH HOH . J 7 HOH A 9 13 13 HOH HOH . J 7 HOH A 10 15 15 HOH HOH . J 7 HOH A 11 16 16 HOH HOH . J 7 HOH A 12 17 17 HOH HOH . J 7 HOH A 13 20 20 HOH HOH . J 7 HOH A 14 22 22 HOH HOH . J 7 HOH A 15 23 23 HOH HOH . J 7 HOH A 16 25 25 HOH HOH . J 7 HOH A 17 29 29 HOH HOH . J 7 HOH A 18 30 30 HOH HOH . J 7 HOH A 19 32 32 HOH HOH . J 7 HOH A 20 34 34 HOH HOH . J 7 HOH A 21 35 35 HOH HOH . J 7 HOH A 22 37 37 HOH HOH . J 7 HOH A 23 39 39 HOH HOH . J 7 HOH A 24 41 41 HOH HOH . J 7 HOH A 25 43 43 HOH HOH . J 7 HOH A 26 44 44 HOH HOH . J 7 HOH A 27 46 46 HOH HOH . J 7 HOH A 28 47 47 HOH HOH . J 7 HOH A 29 48 48 HOH HOH . J 7 HOH A 30 50 50 HOH HOH . J 7 HOH A 31 51 51 HOH HOH . J 7 HOH A 32 55 55 HOH HOH . J 7 HOH A 33 58 58 HOH HOH . J 7 HOH A 34 61 61 HOH HOH . J 7 HOH A 35 67 67 HOH HOH . J 7 HOH A 36 72 72 HOH HOH . J 7 HOH A 37 73 73 HOH HOH . J 7 HOH A 38 75 75 HOH HOH . J 7 HOH A 39 77 77 HOH HOH . J 7 HOH A 40 78 78 HOH HOH . J 7 HOH A 41 80 80 HOH HOH . J 7 HOH A 42 81 81 HOH HOH . J 7 HOH A 43 82 82 HOH HOH . J 7 HOH A 44 83 83 HOH HOH . J 7 HOH A 45 84 84 HOH HOH . J 7 HOH A 46 87 87 HOH HOH . J 7 HOH A 47 88 88 HOH HOH . J 7 HOH A 48 90 90 HOH HOH . J 7 HOH A 49 92 92 HOH HOH . J 7 HOH A 50 93 93 HOH HOH . J 7 HOH A 51 94 94 HOH HOH . J 7 HOH A 52 97 97 HOH HOH . J 7 HOH A 53 98 98 HOH HOH . J 7 HOH A 54 102 102 HOH HOH . J 7 HOH A 55 105 105 HOH HOH . J 7 HOH A 56 106 106 HOH HOH . J 7 HOH A 57 107 107 HOH HOH . J 7 HOH A 58 109 109 HOH HOH . J 7 HOH A 59 110 110 HOH HOH . J 7 HOH A 60 113 113 HOH HOH . J 7 HOH A 61 115 115 HOH HOH . J 7 HOH A 62 117 117 HOH HOH . J 7 HOH A 63 119 119 HOH HOH . J 7 HOH A 64 121 121 HOH HOH . J 7 HOH A 65 123 123 HOH HOH . J 7 HOH A 66 125 125 HOH HOH . J 7 HOH A 67 127 127 HOH HOH . J 7 HOH A 68 128 128 HOH HOH . J 7 HOH A 69 129 129 HOH HOH . J 7 HOH A 70 131 131 HOH HOH . J 7 HOH A 71 132 132 HOH HOH . J 7 HOH A 72 133 133 HOH HOH . J 7 HOH A 73 136 136 HOH HOH . J 7 HOH A 74 137 137 HOH HOH . J 7 HOH A 75 139 139 HOH HOH . J 7 HOH A 76 140 140 HOH HOH . J 7 HOH A 77 143 143 HOH HOH . J 7 HOH A 78 144 144 HOH HOH . J 7 HOH A 79 145 145 HOH HOH . J 7 HOH A 80 149 149 HOH HOH . J 7 HOH A 81 152 152 HOH HOH . J 7 HOH A 82 154 154 HOH HOH . J 7 HOH A 83 155 155 HOH HOH . J 7 HOH A 84 156 156 HOH HOH . J 7 HOH A 85 160 160 HOH HOH . J 7 HOH A 86 161 161 HOH HOH . J 7 HOH A 87 162 162 HOH HOH . J 7 HOH A 88 163 163 HOH HOH . J 7 HOH A 89 164 164 HOH HOH . J 7 HOH A 90 165 165 HOH HOH . J 7 HOH A 91 166 166 HOH HOH . J 7 HOH A 92 169 169 HOH HOH . J 7 HOH A 93 1000 1000 HOH HOH . J 7 HOH A 94 1003 1003 HOH HOH . J 7 HOH A 95 1004 1004 HOH HOH . J 7 HOH A 96 1005 1005 HOH HOH . K 7 HOH B 1 0 0 HOH HOH . K 7 HOH B 2 2 2 HOH HOH . K 7 HOH B 3 3 3 HOH HOH . K 7 HOH B 4 4 4 HOH HOH . K 7 HOH B 5 5 5 HOH HOH . K 7 HOH B 6 6 6 HOH HOH . K 7 HOH B 7 7 7 HOH HOH . K 7 HOH B 8 8 8 HOH HOH . K 7 HOH B 9 11 11 HOH HOH . K 7 HOH B 10 14 14 HOH HOH . K 7 HOH B 11 18 18 HOH HOH . K 7 HOH B 12 19 19 HOH HOH . K 7 HOH B 13 21 21 HOH HOH . K 7 HOH B 14 24 24 HOH HOH . K 7 HOH B 15 26 26 HOH HOH . K 7 HOH B 16 27 27 HOH HOH . K 7 HOH B 17 28 28 HOH HOH . K 7 HOH B 18 31 31 HOH HOH . K 7 HOH B 19 33 33 HOH HOH . K 7 HOH B 20 36 36 HOH HOH . K 7 HOH B 21 38 38 HOH HOH . K 7 HOH B 22 40 40 HOH HOH . K 7 HOH B 23 42 42 HOH HOH . K 7 HOH B 24 45 45 HOH HOH . K 7 HOH B 25 49 49 HOH HOH . K 7 HOH B 26 52 52 HOH HOH . K 7 HOH B 27 53 53 HOH HOH . K 7 HOH B 28 54 54 HOH HOH . K 7 HOH B 29 56 56 HOH HOH . K 7 HOH B 30 57 57 HOH HOH . K 7 HOH B 31 59 59 HOH HOH . K 7 HOH B 32 60 60 HOH HOH . K 7 HOH B 33 62 62 HOH HOH . K 7 HOH B 34 63 63 HOH HOH . K 7 HOH B 35 64 64 HOH HOH . K 7 HOH B 36 65 65 HOH HOH . K 7 HOH B 37 66 66 HOH HOH . K 7 HOH B 38 69 69 HOH HOH . K 7 HOH B 39 70 70 HOH HOH . K 7 HOH B 40 71 71 HOH HOH . K 7 HOH B 41 74 74 HOH HOH . K 7 HOH B 42 76 76 HOH HOH . K 7 HOH B 43 79 79 HOH HOH . K 7 HOH B 44 85 85 HOH HOH . K 7 HOH B 45 86 86 HOH HOH . K 7 HOH B 46 89 89 HOH HOH . K 7 HOH B 47 91 91 HOH HOH . K 7 HOH B 48 95 95 HOH HOH . K 7 HOH B 49 96 96 HOH HOH . K 7 HOH B 50 99 99 HOH HOH . K 7 HOH B 51 100 100 HOH HOH . K 7 HOH B 52 101 101 HOH HOH . K 7 HOH B 53 103 103 HOH HOH . K 7 HOH B 54 104 104 HOH HOH . K 7 HOH B 55 108 108 HOH HOH . K 7 HOH B 56 111 111 HOH HOH . K 7 HOH B 57 112 112 HOH HOH . K 7 HOH B 58 114 114 HOH HOH . K 7 HOH B 59 116 116 HOH HOH . K 7 HOH B 60 118 118 HOH HOH . K 7 HOH B 61 120 120 HOH HOH . K 7 HOH B 62 122 122 HOH HOH . K 7 HOH B 63 124 124 HOH HOH . K 7 HOH B 64 126 126 HOH HOH . K 7 HOH B 65 130 130 HOH HOH . K 7 HOH B 66 134 134 HOH HOH . K 7 HOH B 67 135 135 HOH HOH . K 7 HOH B 68 138 138 HOH HOH . K 7 HOH B 69 141 141 HOH HOH . K 7 HOH B 70 142 142 HOH HOH . K 7 HOH B 71 146 146 HOH HOH . K 7 HOH B 72 147 147 HOH HOH . K 7 HOH B 73 148 148 HOH HOH . K 7 HOH B 74 150 150 HOH HOH . K 7 HOH B 75 151 151 HOH HOH . K 7 HOH B 76 153 153 HOH HOH . K 7 HOH B 77 157 157 HOH HOH . K 7 HOH B 78 158 158 HOH HOH . K 7 HOH B 79 159 159 HOH HOH . K 7 HOH B 80 167 167 HOH HOH . K 7 HOH B 81 168 168 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 N9 IBM . . . H 5 97.565 19.832 12.524 1 58.8 ? N9 IBM 900 B 1 HETATM 2 C C8 IBM . . . H 5 97.872 19.619 11.19 1 58.74 ? C8 IBM 900 B 1 HETATM 3 N N7 IBM . . . H 5 97.563 20.706 10.407 1 56.99 ? N7 IBM 900 B 1 HETATM 4 C C5 IBM . . . H 5 97.024 21.617 11.242 1 57.89 ? C5 IBM 900 B 1 HETATM 5 C C4 IBM . . . H 5 97.035 21.067 12.581 1 58.72 ? C4 IBM 900 B 1 HETATM 6 N N3 IBM . . . H 5 96.542 21.711 13.69 1 58.61 ? N3 IBM 900 B 1 HETATM 7 C C2 IBM . . . H 5 96.053 23.015 13.446 1 60.72 ? C2 IBM 900 B 1 HETATM 8 N N1 IBM . . . H 5 96.032 23.645 12.095 1 58.86 ? N1 IBM 900 B 1 HETATM 9 C C6 IBM . . . H 5 96.516 22.912 10.999 1 58.02 ? C6 IBM 900 B 1 HETATM 10 O O6 IBM . . . H 5 96.546 23.309 9.788 1 57.39 ? O6 IBM 900 B 1 HETATM 11 O O2 IBM . . . H 5 95.56 23.664 14.425 1 59.54 ? O2 IBM 900 B 1 HETATM 12 C C10 IBM . . . H 5 95.481 25.022 11.962 1 57.5 ? C10 IBM 900 B 1 HETATM 13 C C11 IBM . . . H 5 96.592 21.166 15.068 1 58.18 ? C11 IBM 900 B 1 HETATM 14 C C12 IBM . . . H 5 95.538 20.171 15.587 1 61.75 ? C12 IBM 900 B 1 HETATM 15 C C13 IBM . . . H 5 95.569 18.85 14.783 1 62.55 ? C13 IBM 900 B 1 HETATM 16 C C14 IBM . . . H 5 94.118 20.773 15.748 1 63.63 ? C14 IBM 900 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #