data_8DIO # _model_server_result.job_id jr8KZLGItjLtuW_MfARGKA _model_server_result.datetime_utc '2024-10-22 17:51:16' _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 8dio # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 8DIO # _exptl.entry_id 8DIO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 763.416 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate' _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 100.307 _cell.angle_gamma 90 _cell.entry_id 8DIO _cell.length_a 47.95 _cell.length_b 59.702 _cell.length_c 60.381 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DIO _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E 1 1 B,D,F 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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H30 N8 O18 P3 1' _chem_comp.formula_weight 763.416 _chem_comp.id 91P _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dinucleotide triphosphate cap analog m7GpppC' # 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 O45 C44 91P doub 1 n n N46 C44 91P sing 2 n n N46 C47 91P sing 3 n n N37 C33 91P sing 4 n n C44 C43 91P sing 5 n n N49 C47 91P sing 6 n n C47 N48 91P doub 7 n n C33 N34 91P doub 8 n n C33 C32 91P sing 9 n n C43 N02 91P sing 10 n y C43 C42 91P doub 11 n y C01 N02 91P sing 12 n n N34 C35 91P sing 13 n n N48 C42 91P sing 14 n n N02 C03 91P sing 15 n y C32 C31 91P doub 16 n n C42 N04 91P sing 17 n y C35 O36 91P doub 18 n n C35 N30 91P sing 19 n n C03 N04 91P doub 20 n y C31 N30 91P sing 21 n n N04 C05 91P sing 22 n n N30 C25 91P sing 23 n n C05 O06 91P sing 24 n n C05 C40 91P sing 25 n n C25 O24 91P sing 26 n n C25 C26 91P sing 27 n n O06 C07 91P sing 28 n n O41 C40 91P sing 29 n n C40 C38 91P sing 30 n n O24 C23 91P sing 31 n n O27 C26 91P sing 32 n n C26 C28 91P sing 33 n n O09 P10 91P sing 34 n n O09 C08 91P sing 35 n n O12 P10 91P doub 36 n n O11 P10 91P sing 37 n n C07 C08 91P sing 38 n n C07 C38 91P sing 39 n n P10 O13 91P sing 40 n n C38 O39 91P sing 41 n n C23 C28 91P sing 42 n n C23 C22 91P sing 43 n n C28 O29 91P sing 44 n n C22 O21 91P sing 45 n n O13 P14 91P sing 46 n n O17 P14 91P sing 47 n n O17 P18 91P sing 48 n n O21 P18 91P sing 49 n n O16 P14 91P doub 50 n n O20 P18 91P doub 51 n n P14 O15 91P sing 52 n n P18 O19 91P sing 53 n n C22 H221 91P sing 54 n n C22 H222 91P sing 55 n n C26 H261 91P sing 56 n n C28 H281 91P sing 57 n n C01 H011 91P sing 58 n n C01 H013 91P sing 59 n n C01 H012 91P sing 60 n n C03 H031 91P sing 61 n n C05 H051 91P sing 62 n n C07 H071 91P sing 63 n n C08 H082 91P sing 64 n n C08 H081 91P sing 65 n n C23 H231 91P sing 66 n n C25 H251 91P sing 67 n n C31 H311 91P sing 68 n n C32 H321 91P sing 69 n n C38 H381 91P sing 70 n n C40 H401 91P sing 71 n n N37 H371 91P sing 72 n n N37 H372 91P sing 73 n n N46 H461 91P sing 74 n n N49 H491 91P sing 75 n n N49 H492 91P sing 76 n n O11 H1 91P sing 77 n n O15 H2 91P sing 78 n n O19 H3 91P sing 79 n n O27 H271 91P sing 80 n n O29 H291 91P sing 81 n n O39 H391 91P sing 82 n n O41 H411 91P sing 83 n n # _atom_sites.entry_id 8DIO _atom_sites.fract_transf_matrix[1][1] 0.020855 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003793 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01675 _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] 0.016833 _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 91P A 1 1001 1001 91P 91P . D 3 MY6 B 1 1001 1001 MY6 MY6 . E 4 HOH A 1 1101 55 HOH HOH . E 4 HOH A 2 1102 90 HOH HOH . E 4 HOH A 3 1103 54 HOH HOH . E 4 HOH A 4 1104 83 HOH HOH . E 4 HOH A 5 1105 45 HOH HOH . E 4 HOH A 6 1106 3 HOH HOH . E 4 HOH A 7 1107 88 HOH HOH . E 4 HOH A 8 1108 14 HOH HOH . E 4 HOH A 9 1109 38 HOH HOH . E 4 HOH A 10 1110 37 HOH HOH . E 4 HOH A 11 1111 1 HOH HOH . E 4 HOH A 12 1112 27 HOH HOH . E 4 HOH A 13 1113 63 HOH HOH . E 4 HOH A 14 1114 66 HOH HOH . E 4 HOH A 15 1115 5 HOH HOH . E 4 HOH A 16 1116 44 HOH HOH . E 4 HOH A 17 1117 93 HOH HOH . E 4 HOH A 18 1118 6 HOH HOH . E 4 HOH A 19 1119 29 HOH HOH . E 4 HOH A 20 1120 84 HOH HOH . E 4 HOH A 21 1121 67 HOH HOH . E 4 HOH A 22 1122 41 HOH HOH . E 4 HOH A 23 1123 47 HOH HOH . E 4 HOH A 24 1124 4 HOH HOH . E 4 HOH A 25 1125 36 HOH HOH . E 4 HOH A 26 1126 30 HOH HOH . E 4 HOH A 27 1127 70 HOH HOH . E 4 HOH A 28 1128 22 HOH HOH . E 4 HOH A 29 1129 2 HOH HOH . E 4 HOH A 30 1130 76 HOH HOH . E 4 HOH A 31 1131 50 HOH HOH . E 4 HOH A 32 1132 51 HOH HOH . E 4 HOH A 33 1133 89 HOH HOH . E 4 HOH A 34 1134 18 HOH HOH . E 4 HOH A 35 1135 68 HOH HOH . E 4 HOH A 36 1136 39 HOH HOH . E 4 HOH A 37 1137 49 HOH HOH . E 4 HOH A 38 1138 58 HOH HOH . E 4 HOH A 39 1139 25 HOH HOH . E 4 HOH A 40 1140 32 HOH HOH . E 4 HOH A 41 1141 20 HOH HOH . E 4 HOH A 42 1142 48 HOH HOH . E 4 HOH A 43 1143 91 HOH HOH . E 4 HOH A 44 1144 92 HOH HOH . E 4 HOH A 45 1145 71 HOH HOH . E 4 HOH A 46 1146 82 HOH HOH . E 4 HOH A 47 1147 75 HOH HOH . E 4 HOH A 48 1148 81 HOH HOH . E 4 HOH A 49 1149 86 HOH HOH . F 4 HOH B 1 1101 80 HOH HOH . F 4 HOH B 2 1102 72 HOH HOH . F 4 HOH B 3 1103 73 HOH HOH . F 4 HOH B 4 1104 31 HOH HOH . F 4 HOH B 5 1105 77 HOH HOH . F 4 HOH B 6 1106 42 HOH HOH . F 4 HOH B 7 1107 87 HOH HOH . F 4 HOH B 8 1108 64 HOH HOH . F 4 HOH B 9 1109 26 HOH HOH . F 4 HOH B 10 1110 33 HOH HOH . F 4 HOH B 11 1111 46 HOH HOH . F 4 HOH B 12 1112 52 HOH HOH . F 4 HOH B 13 1113 56 HOH HOH . F 4 HOH B 14 1114 43 HOH HOH . F 4 HOH B 15 1115 7 HOH HOH . F 4 HOH B 16 1116 61 HOH HOH . F 4 HOH B 17 1117 8 HOH HOH . F 4 HOH B 18 1118 78 HOH HOH . F 4 HOH B 19 1119 53 HOH HOH . F 4 HOH B 20 1120 62 HOH HOH . F 4 HOH B 21 1121 85 HOH HOH . F 4 HOH B 22 1122 28 HOH HOH . F 4 HOH B 23 1123 74 HOH HOH . F 4 HOH B 24 1124 57 HOH HOH . F 4 HOH B 25 1125 79 HOH HOH . F 4 HOH B 26 1126 40 HOH HOH . F 4 HOH B 27 1127 60 HOH HOH . F 4 HOH B 28 1128 59 HOH HOH . F 4 HOH B 29 1129 35 HOH HOH . F 4 HOH B 30 1130 65 HOH HOH . F 4 HOH B 31 1131 69 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 C C22 91P . . . C 2 -2.695 10.232 -18.542 1 30.88 ? C22 91P 1001 A 1 HETATM 2 C C26 91P . . . C 2 0.838 9.401 -18.741 1 33.01 ? C26 91P 1001 A 1 HETATM 3 C C28 91P . . . C 2 -0.329 10.014 -19.323 1 32.74 ? C28 91P 1001 A 1 HETATM 4 C C01 91P . . . C 2 -5.426 4.494 -23.252 1 39.3 ? C01 91P 1001 A 1 HETATM 5 C C03 91P . . . C 2 -6.223 6.819 -22.178 1 35.5 ? C03 91P 1001 A 1 HETATM 6 C C05 91P . . . C 2 -7.178 8.064 -20.213 1 32.56 ? C05 91P 1001 A 1 HETATM 7 C C07 91P . . . C 2 -8.06 10.023 -21.283 1 33.04 ? C07 91P 1001 A 1 HETATM 8 C C08 91P . . . C 2 -7.586 10.267 -22.695 1 33.84 ? C08 91P 1001 A 1 HETATM 9 C C23 91P . . . C 2 -1.288 9.995 -18.271 1 31.25 ? C23 91P 1001 A 1 HETATM 10 C C25 91P . . . C 2 0.446 8.359 -17.825 1 32.41 ? C25 91P 1001 A 1 HETATM 11 C C31 91P . . . C 2 0.592 6.503 -19.553 1 35.44 ? C31 91P 1001 A 1 HETATM 12 C C32 91P . . . C 2 0.68 5.241 -19.997 1 37 ? C32 91P 1001 A 1 HETATM 13 C C33 91P . . . C 2 0.705 4.222 -18.915 1 36.33 ? C33 91P 1001 A 1 HETATM 14 C C35 91P . . . C 2 0.553 6.271 -17.393 1 33.18 ? C35 91P 1001 A 1 HETATM 15 C C38 91P . . . C 2 -6.976 10.413 -20.351 1 31.74 ? C38 91P 1001 A 1 HETATM 16 C C40 91P . . . C 2 -6.179 9.185 -20.094 1 31.71 ? C40 91P 1001 A 1 HETATM 17 C C42 91P . . . C 2 -6.824 5.667 -20.132 1 34.19 ? C42 91P 1001 A 1 HETATM 18 C C43 91P . . . C 2 -6.359 4.566 -20.828 1 35.95 ? C43 91P 1001 A 1 HETATM 19 C C44 91P . . . C 2 -6.343 3.223 -20.293 1 36.84 ? C44 91P 1001 A 1 HETATM 20 C C47 91P . . . C 2 -7.227 4.034 -18.338 1 34.05 ? C47 91P 1001 A 1 HETATM 21 N N02 91P . . . C 2 -5.957 5.242 -22.127 1 36.99 ? N02 91P 1001 A 1 HETATM 22 N N04 91P . . . C 2 -6.733 6.833 -20.838 1 33.97 ? N04 91P 1001 A 1 HETATM 23 N N30 91P . . . C 2 0.562 6.981 -18.149 1 33.56 ? N30 91P 1001 A 1 HETATM 24 N N34 91P . . . C 2 0.632 4.894 -17.48 1 34.18 ? N34 91P 1001 A 1 HETATM 25 N N37 91P . . . C 2 0.798 2.756 -19.007 1 38.13 ? N37 91P 1001 A 1 HETATM 26 N N46 91P . . . C 2 -6.763 3.003 -19.105 1 35.59 ? N46 91P 1001 A 1 HETATM 27 N N48 91P . . . C 2 -7.309 5.389 -18.709 1 33.22 ? N48 91P 1001 A 1 HETATM 28 N N49 91P . . . C 2 -7.696 3.656 -17.028 1 33.2 ? N49 91P 1001 A 1 HETATM 29 O O06 91P . . . C 2 -8.311 8.593 -21.02 1 33.36 ? O06 91P 1001 A 1 HETATM 30 O O09 91P . . . C 2 -6.287 9.694 -22.835 1 34.46 ? O09 91P 1001 A 1 HETATM 31 O O11 91P . . . C 2 -4.14 9.686 -24.288 1 36.98 ? O11 91P 1001 A 1 HETATM 32 O O12 91P . . . C 2 -5.315 11.683 -24.181 1 35.52 ? O12 91P 1001 A 1 HETATM 33 O O13 91P . . . C 2 -3.98 11.189 -22.115 1 33.83 ? O13 91P 1001 A 1 HETATM 34 O O15 91P . . . C 2 -5.551 13.28 -22.212 1 32.56 ? O15 91P 1001 A 1 HETATM 35 O O16 91P . . . C 2 -3.307 13.523 -22.887 1 33.34 ? O16 91P 1001 A 1 HETATM 36 O O17 91P . . . C 2 -3.828 13.273 -20.277 1 31.38 ? O17 91P 1001 A 1 HETATM 37 O O19 91P . . . C 2 -2.054 11.734 -20.465 1 32.37 ? O19 91P 1001 A 1 HETATM 38 O O20 91P . . . C 2 -1.482 13.436 -19.064 1 30.62 ? O20 91P 1001 A 1 HETATM 39 O O21 91P . . . C 2 -3.018 11.588 -18.141 1 29.54 ? O21 91P 1001 A 1 HETATM 40 O O24 91P . . . C 2 -1.174 8.54 -17.709 1 31.55 ? O24 91P 1001 A 1 HETATM 41 O O27 91P . . . C 2 1.506 10.417 -17.887 1 32.39 ? O27 91P 1001 A 1 HETATM 42 O O29 91P . . . C 2 -0.085 11.438 -19.609 1 32.85 ? O29 91P 1001 A 1 HETATM 43 O O36 91P . . . C 2 0.492 6.675 -16.035 1 31.46 ? O36 91P 1001 A 1 HETATM 44 O O39 91P . . . C 2 -7.526 10.857 -19.088 1 31.27 ? O39 91P 1001 A 1 HETATM 45 O O41 91P . . . C 2 -5.596 9.357 -18.773 1 30.68 ? O41 91P 1001 A 1 HETATM 46 O O45 91P . . . C 2 -5.886 2.134 -21.04 1 38.9 ? O45 91P 1001 A 1 HETATM 47 P P10 91P . . . C 2 -4.897 10.531 -23.333 1 35.93 ? P10 91P 1001 A 1 HETATM 48 P P14 91P . . . C 2 -4.159 12.837 -21.886 1 33.09 ? P14 91P 1001 A 1 HETATM 49 P P18 91P . . . C 2 -2.612 12.579 -19.389 1 30.77 ? P18 91P 1001 A 1 HETATM 50 H H221 91P . . . C 2 -3.3 9.529 -17.978 1 26.33 ? H221 91P 1001 A 1 HETATM 51 H H222 91P . . . C 2 -2.89 10.107 -19.602 1 26.33 ? H222 91P 1001 A 1 HETATM 52 H H261 91P . . . C 2 1.46 9.012 -19.543 1 19.23 ? H261 91P 1001 A 1 HETATM 53 H H281 91P . . . C 2 -0.619 9.501 -20.229 1 24.29 ? H281 91P 1001 A 1 HETATM 54 H H011 91P . . . C 2 -4.39 4.775 -23.416 1 25.39 ? H011 91P 1001 A 1 HETATM 55 H H013 91P . . . C 2 -6.008 4.718 -24.141 1 25.39 ? H013 91P 1001 A 1 HETATM 56 H H012 91P . . . C 2 -5.485 3.431 -23.039 1 25.39 ? H012 91P 1001 A 1 HETATM 57 H H031 91P . . . C 2 -6.075 7.578 -22.929 1 15.46 ? H031 91P 1001 A 1 HETATM 58 H H051 91P . . . C 2 -7.422 7.812 -19.194 1 17.71 ? H051 91P 1001 A 1 HETATM 59 H H071 91P . . . C 2 -8.977 10.584 -21.123 1 20.5 ? H071 91P 1001 A 1 HETATM 60 H H082 91P . . . C 2 -7.54 11.332 -22.887 1 30.67 ? H082 91P 1001 A 1 HETATM 61 H H081 91P . . . C 2 -8.269 9.803 -23.396 1 30.67 ? H081 91P 1001 A 1 HETATM 62 H H231 91P . . . C 2 -1.036 10.844 -17.633 1 23.21 ? H231 91P 1001 A 1 HETATM 63 H H251 91P . . . C 2 1.116 8.508 -16.99 1 18.51 ? H251 91P 1001 A 1 HETATM 64 H H311 91P . . . C 2 0.901 7.256 -20.275 1 20.92 ? H311 91P 1001 A 1 HETATM 65 H H321 91P . . . C 2 0.407 4.981 -21.014 1 22.41 ? H321 91P 1001 A 1 HETATM 66 H H381 91P . . . C 2 -6.38 11.199 -20.8 1 21.57 ? H381 91P 1001 A 1 HETATM 67 H H401 91P . . . C 2 -5.377 8.977 -20.792 1 15.94 ? H401 91P 1001 A 1 HETATM 68 H H371 91P . . . C 2 0.006 2.194 -19.161 1 23.88 ? H371 91P 1001 A 1 HETATM 69 H H372 91P . . . C 2 1.737 2.309 -18.882 1 23.88 ? H372 91P 1001 A 1 HETATM 70 H H461 91P . . . C 2 -6.751 2.076 -18.738 1 4.53 ? H461 91P 1001 A 1 HETATM 71 H H491 91P . . . C 2 -8.433 4.172 -16.592 1 0 ? H491 91P 1001 A 1 HETATM 72 H H492 91P . . . C 2 -7.3 2.837 -16.571 1 0 ? H492 91P 1001 A 1 HETATM 73 H H271 91P . . . C 2 1.001 10.534 -17.094 1 25.74 ? H271 91P 1001 A 1 HETATM 74 H H291 91P . . . C 2 0.363 11.842 -18.893 1 34.51 ? H291 91P 1001 A 1 HETATM 75 H H391 91P . . . C 2 -8.114 10.197 -18.748 1 19.54 ? H391 91P 1001 A 1 HETATM 76 H H411 91P . . . C 2 -5.047 8.604 -18.572 1 21.33 ? H411 91P 1001 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 76 #