data_8DHU # _model_server_result.job_id NqpfL3657pxZe4e6aGhsPg _model_server_result.datetime_utc '2024-10-22 21:03:36' _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 8dhu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 8DHU # _exptl.entry_id 8DHU _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 90 _cell.angle_gamma 90 _cell.entry_id 8DHU _cell.length_a 46.808 _cell.length_b 60.737 _cell.length_c 129.199 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DHU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # 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,E 1 1 B,C,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 8DHU _atom_sites.fract_transf_matrix[1][1] 0.021364 _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] 0.016464 _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] 0.00774 _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 B 1 1001 1001 91P 91P . D 3 MG B 1 1002 1 MG MG . E 4 HOH A 1 1001 61 HOH HOH . E 4 HOH A 2 1002 64 HOH HOH . E 4 HOH A 3 1003 65 HOH HOH . E 4 HOH A 4 1004 23 HOH HOH . E 4 HOH A 5 1005 4 HOH HOH . E 4 HOH A 6 1006 45 HOH HOH . E 4 HOH A 7 1007 51 HOH HOH . E 4 HOH A 8 1008 29 HOH HOH . E 4 HOH A 9 1009 25 HOH HOH . E 4 HOH A 10 1010 57 HOH HOH . E 4 HOH A 11 1011 2 HOH HOH . E 4 HOH A 12 1012 20 HOH HOH . E 4 HOH A 13 1013 33 HOH HOH . E 4 HOH A 14 1014 19 HOH HOH . E 4 HOH A 15 1015 52 HOH HOH . E 4 HOH A 16 1016 47 HOH HOH . E 4 HOH A 17 1017 3 HOH HOH . E 4 HOH A 18 1018 56 HOH HOH . E 4 HOH A 19 1019 18 HOH HOH . E 4 HOH A 20 1020 13 HOH HOH . E 4 HOH A 21 1021 30 HOH HOH . E 4 HOH A 22 1022 22 HOH HOH . E 4 HOH A 23 1023 55 HOH HOH . E 4 HOH A 24 1024 14 HOH HOH . E 4 HOH A 25 1025 21 HOH HOH . E 4 HOH A 26 1026 32 HOH HOH . E 4 HOH A 27 1027 38 HOH HOH . E 4 HOH A 28 1028 27 HOH HOH . E 4 HOH A 29 1029 63 HOH HOH . E 4 HOH A 30 1030 49 HOH HOH . E 4 HOH A 31 1031 43 HOH HOH . E 4 HOH A 32 1032 42 HOH HOH . F 4 HOH B 1 1101 6 HOH HOH . F 4 HOH B 2 1102 12 HOH HOH . F 4 HOH B 3 1103 50 HOH HOH . F 4 HOH B 4 1104 35 HOH HOH . F 4 HOH B 5 1105 10 HOH HOH . F 4 HOH B 6 1106 17 HOH HOH . F 4 HOH B 7 1107 53 HOH HOH . F 4 HOH B 8 1108 11 HOH HOH . F 4 HOH B 9 1109 59 HOH HOH . F 4 HOH B 10 1110 1 HOH HOH . F 4 HOH B 11 1111 46 HOH HOH . F 4 HOH B 12 1112 5 HOH HOH . F 4 HOH B 13 1113 66 HOH HOH . F 4 HOH B 14 1114 58 HOH HOH . F 4 HOH B 15 1115 15 HOH HOH . F 4 HOH B 16 1116 24 HOH HOH . F 4 HOH B 17 1117 31 HOH HOH . F 4 HOH B 18 1118 8 HOH HOH . F 4 HOH B 19 1119 48 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 13.132 -23.504 -10.822 1 84.04 ? C22 91P 1001 B 1 HETATM 2 C C26 91P . . . C 2 13.7 -26.452 -9.892 1 70.73 ? C26 91P 1001 B 1 HETATM 3 C C28 91P . . . C 2 13.649 -25.876 -11.047 1 74.09 ? C28 91P 1001 B 1 HETATM 4 C C01 91P . . . C 2 11.755 -20.323 -3.259 1 78.4 ? C01 91P 1001 B 1 HETATM 5 C C03 91P . . . C 2 12.681 -19.537 -5.418 1 77.13 ? C03 91P 1001 B 1 HETATM 6 C C05 91P . . . C 2 13.911 -18.761 -7.282 1 77.86 ? C05 91P 1001 B 1 HETATM 7 C C07 91P . . . C 2 12.455 -17.668 -8.826 1 90.25 ? C07 91P 1001 B 1 HETATM 8 C C08 91P . . . C 2 10.972 -18.137 -8.908 1 94.24 ? C08 91P 1001 B 1 HETATM 9 C C23 91P . . . C 2 14.185 -24.427 -10.823 1 71.83 ? C23 91P 1001 B 1 HETATM 10 C C25 91P . . . C 2 15.033 -25.826 -9.179 1 69.23 ? C25 91P 1001 B 1 HETATM 11 C C31 91P . . . C 2 14.035 -25.443 -6.882 1 72.09 ? C31 91P 1001 B 1 HETATM 12 C C32 91P . . . C 2 14.19 -25.694 -5.406 1 74.21 ? C32 91P 1001 B 1 HETATM 13 C C33 91P . . . C 2 15.338 -26.482 -4.829 1 72.29 ? C33 91P 1001 B 1 HETATM 14 C C35 91P . . . C 2 16.188 -26.787 -7.218 1 67.78 ? C35 91P 1001 B 1 HETATM 15 C C38 91P . . . C 2 13.51 -18.65 -9.396 1 87.2 ? C38 91P 1001 B 1 HETATM 16 C C40 91P . . . C 2 13.792 -19.597 -8.236 1 86.45 ? C40 91P 1001 B 1 HETATM 17 C C42 91P . . . C 2 14.75 -19.396 -4.933 1 77.62 ? C42 91P 1001 B 1 HETATM 18 C C43 91P . . . C 2 14.115 -19.848 -3.834 1 79.09 ? C43 91P 1001 B 1 HETATM 19 C C44 91P . . . C 2 14.98 -20.134 -2.604 1 68.66 ? C44 91P 1001 B 1 HETATM 20 C C47 91P . . . C 2 17.088 -19.45 -3.825 1 73.7 ? C47 91P 1001 B 1 HETATM 21 N N02 91P . . . C 2 12.83 -19.918 -4.132 1 85.51 ? N02 91P 1001 B 1 HETATM 22 N N04 91P . . . C 2 13.891 -19.211 -5.902 1 78.1 ? N04 91P 1001 B 1 HETATM 23 N N30 91P . . . C 2 15.043 -26 -7.767 1 72.54 ? N30 91P 1001 B 1 HETATM 24 N N34 91P . . . C 2 16.323 -27.023 -5.759 1 61.21 ? N34 91P 1001 B 1 HETATM 25 N N37 91P . . . C 2 15.475 -26.729 -3.379 1 65.89 ? N37 91P 1001 B 1 HETATM 26 N N46 91P . . . C 2 16.418 -19.934 -2.627 1 64.55 ? N46 91P 1001 B 1 HETATM 27 N N48 91P . . . C 2 16.234 -19.184 -4.972 1 71.03 ? N48 91P 1001 B 1 HETATM 28 N N49 91P . . . C 2 18.537 -19.203 -3.997 1 64.96 ? N49 91P 1001 B 1 HETATM 29 O O06 91P . . . C 2 12.877 -17.54 -7.602 1 77.99 ? O06 91P 1001 B 1 HETATM 30 O O09 91P . . . C 2 10.703 -19.136 -7.969 1 93.38 ? O09 91P 1001 B 1 HETATM 31 O O11 91P . . . C 2 8.394 -19.735 -8.946 1 109.03 -1 O11 91P 1001 B 1 HETATM 32 O O12 91P . . . C 2 9.292 -21.133 -7.129 1 135.49 ? O12 91P 1001 B 1 HETATM 33 O O13 91P . . . C 2 10.269 -21.332 -9.547 1 120.03 ? O13 91P 1001 B 1 HETATM 34 O O15 91P . . . C 2 9.351 -19.883 -11.494 1 103.53 -1 O15 91P 1001 B 1 HETATM 35 O O16 91P . . . C 2 9.707 -22.284 -11.952 1 80.48 ? O16 91P 1001 B 1 HETATM 36 O O17 91P . . . C 2 11.76 -20.847 -11.721 1 107.85 ? O17 91P 1001 B 1 HETATM 37 O O19 91P . . . C 2 11.736 -22.02 -14.025 1 86.33 -1 O19 91P 1001 B 1 HETATM 38 O O20 91P . . . C 2 13.909 -21.241 -13.124 1 86.28 ? O20 91P 1001 B 1 HETATM 39 O O21 91P . . . C 2 12.772 -23.334 -12.16 1 87.27 ? O21 91P 1001 B 1 HETATM 40 O O24 91P . . . C 2 14.944 -24.561 -9.499 1 65.88 ? O24 91P 1001 B 1 HETATM 41 O O27 91P . . . C 2 13.774 -27.855 -10.224 1 63.7 ? O27 91P 1001 B 1 HETATM 42 O O29 91P . . . C 2 14.588 -26.555 -12.016 1 54.39 ? O29 91P 1001 B 1 HETATM 43 O O36 91P . . . C 2 17.02 -27.24 -7.937 1 54.97 ? O36 91P 1001 B 1 HETATM 44 O O39 91P . . . C 2 14.619 -17.887 -9.65 1 82.32 ? O39 91P 1001 B 1 HETATM 45 O O41 91P . . . C 2 15.09 -20.306 -8.467 1 68.74 ? O41 91P 1001 B 1 HETATM 46 O O45 91P . . . C 2 14.474 -20.533 -1.611 1 72.63 ? O45 91P 1001 B 1 HETATM 47 P P10 91P . . . C 2 9.646 -20.346 -8.374 1 88.7 ? P10 91P 1001 B 1 HETATM 48 P P14 91P . . . C 2 10.218 -21.084 -11.191 1 94.45 ? P14 91P 1001 B 1 HETATM 49 P P18 91P . . . C 2 12.56 -21.836 -12.777 1 75.7 ? P18 91P 1001 B 1 HETATM 50 H H221 91P . . . C 2 12.382 -23.849 -10.313 1 100.65 ? H221 91P 1001 B 1 HETATM 51 H H222 91P . . . C 2 13.422 -22.661 -10.441 1 100.65 ? H222 91P 1001 B 1 HETATM 52 H H261 91P . . . C 2 12.972 -26.276 -9.276 1 84.67 ? H261 91P 1001 B 1 HETATM 53 H H281 91P . . . C 2 12.731 -25.88 -11.361 1 88.71 ? H281 91P 1001 B 1 HETATM 54 H H011 91P . . . C 2 11.795 -21.282 -3.12 1 93.88 ? H011 91P 1001 B 1 HETATM 55 H H013 91P . . . C 2 11.842 -19.869 -2.406 1 93.88 ? H013 91P 1001 B 1 HETATM 56 H H012 91P . . . C 2 10.904 -20.09 -3.664 1 93.88 ? H012 91P 1001 B 1 HETATM 57 H H031 91P . . . C 2 11.879 -19.505 -5.888 1 92.36 ? H031 91P 1001 B 1 HETATM 58 H H051 91P . . . C 2 14.832 -18.467 -7.357 1 93.23 ? H051 91P 1001 B 1 HETATM 59 H H071 91P . . . C 2 12.468 -16.838 -9.326 1 108.1 ? H071 91P 1001 B 1 HETATM 60 H H082 91P . . . C 2 10.39 -17.38 -8.739 1 112.89 ? H082 91P 1001 B 1 HETATM 61 H H081 91P . . . C 2 10.799 -18.485 -9.797 1 112.89 ? H081 91P 1001 B 1 HETATM 62 H H231 91P . . . C 2 14.802 -24.126 -11.508 1 85.99 ? H231 91P 1001 B 1 HETATM 63 H H251 91P . . . C 2 15.838 -26.245 -9.521 1 82.88 ? H251 91P 1001 B 1 HETATM 64 H H311 91P . . . C 2 13.321 -24.95 -7.215 1 86.31 ? H311 91P 1001 B 1 HETATM 65 H H321 91P . . . C 2 13.551 -25.348 -4.826 1 88.85 ? H321 91P 1001 B 1 HETATM 66 H H381 91P . . . C 2 13.207 -19.151 -10.17 1 104.44 ? H381 91P 1001 B 1 HETATM 67 H H401 91P . . . C 2 13.092 -20.252 -8.088 1 103.54 ? H401 91P 1001 B 1 HETATM 68 H H371 91P . . . C 2 16.167 -27.298 -3.127 1 78.87 ? H371 91P 1001 B 1 HETATM 69 H H372 91P . . . C 2 14.879 -26.285 -2.815 1 78.87 ? H372 91P 1001 B 1 HETATM 70 H H461 91P . . . C 2 16.88 -20.104 -1.923 1 77.27 ? H461 91P 1001 B 1 HETATM 71 H H491 91P . . . C 2 19.104 -19.28 -3.244 1 77.76 ? H491 91P 1001 B 1 HETATM 72 H H492 91P . . . C 2 18.784 -18.974 -4.876 1 77.76 ? H492 91P 1001 B 1 HETATM 73 H H271 91P . . . C 2 14.559 -27.993 -10.456 1 76.24 ? H271 91P 1001 B 1 HETATM 74 H H291 91P . . . C 2 14.958 -25.992 -12.537 1 65.08 ? H291 91P 1001 B 1 HETATM 75 H H391 91P . . . C 2 14.555 -17.144 -9.252 1 98.59 ? H391 91P 1001 B 1 HETATM 76 H H411 91P . . . C 2 15.026 -20.839 -9.13 1 82.29 ? H411 91P 1001 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 76 #