data_7V8J # _model_server_result.job_id ZjA2T4brcaOr2-nqdFempQ _model_server_result.datetime_utc '2025-01-09 02:29:55' _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 7v8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 7V8J # _exptl.entry_id 7V8J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.336 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" _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 102.55 _cell.angle_gamma 90 _cell.entry_id 7V8J _cell.length_a 77.08 _cell.length_b 81.72 _cell.length_c 105.26 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7V8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 # _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 'C15 H21 N6 O8 P' _chem_comp.formula_weight 444.336 _chem_comp.id PR8 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms prolyl-adenylate # 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 O10 C PR8 sing 281 n n C O PR8 doub 282 n n C CA PR8 sing 283 n n CA N PR8 sing 284 n n CD N PR8 sing 285 n n N HN PR8 sing 286 n n O2P P PR8 doub 287 n n O5' P PR8 sing 288 n n P O1P PR8 sing 289 n n P O10 PR8 sing 290 n n C2 N1 PR8 doub 291 n y N1 C6 PR8 sing 292 n y C2 N3 PR8 sing 293 n y C2 H2 PR8 sing 294 n n N3 C4 PR8 doub 295 n y C4 N9 PR8 sing 296 n y C4 C5 PR8 sing 297 n y C6 C5 PR8 doub 298 n y C5 N7 PR8 sing 299 n y C6 N6 PR8 sing 300 n n N6 HN6 PR8 sing 301 n n N6 HN6A PR8 sing 302 n n C8 N7 PR8 doub 303 n y N9 C8 PR8 sing 304 n y C8 H8 PR8 sing 305 n n C1' N9 PR8 sing 306 n n CB CA PR8 sing 307 n n CA HA PR8 sing 308 n n CB CG PR8 sing 309 n n CB HB PR8 sing 310 n n CB HBA PR8 sing 311 n n CG CD PR8 sing 312 n n CD HD PR8 sing 313 n n CD HDA PR8 sing 314 n n CG HG PR8 sing 315 n n CG HGA PR8 sing 316 n n C2' C1' PR8 sing 317 n n C1' O4' PR8 sing 318 n n C1' H1' PR8 sing 319 n n O1P HO1P PR8 sing 320 n n O2' C2' PR8 sing 321 n n C2' C3' PR8 sing 322 n n C2' H2' PR8 sing 323 n n O2' HO2' PR8 sing 324 n n O3' C3' PR8 sing 325 n n C3' C4' PR8 sing 326 n n C3' H3' PR8 sing 327 n n O3' HO3' PR8 sing 328 n n C4' O4' PR8 sing 329 n n C4' C5' PR8 sing 330 n n C4' H4' PR8 sing 331 n n C5' O5' PR8 sing 332 n n C5' H5' PR8 sing 333 n n C5' "H5'A" PR8 sing 334 n n # _atom_sites.entry_id 7V8J _atom_sites.fract_transf_matrix[1][1] 0.012974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002888 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012237 _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] 0.009733 _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 PR8 A 1 901 901 PR8 PDS . D 3 PPV A 1 902 902 PPV PPV . E 4 EDO A 1 903 1001 EDO EDO . F 4 EDO A 1 904 1002 EDO EDO . G 5 PRO B 1 901 902 PRO PRO . H 4 EDO B 1 902 1001 EDO EDO . I 4 EDO B 1 903 1002 EDO EDO . J 6 HOH A 1 1001 71 HOH HOH . J 6 HOH A 2 1002 131 HOH HOH . J 6 HOH A 3 1003 45 HOH HOH . J 6 HOH A 4 1004 64 HOH HOH . J 6 HOH A 5 1005 9 HOH HOH . J 6 HOH A 6 1006 128 HOH HOH . J 6 HOH A 7 1007 13 HOH HOH . J 6 HOH A 8 1008 104 HOH HOH . J 6 HOH A 9 1009 19 HOH HOH . J 6 HOH A 10 1010 24 HOH HOH . J 6 HOH A 11 1011 6 HOH HOH . J 6 HOH A 12 1012 2 HOH HOH . J 6 HOH A 13 1013 8 HOH HOH . J 6 HOH A 14 1014 155 HOH HOH . J 6 HOH A 15 1015 27 HOH HOH . J 6 HOH A 16 1016 106 HOH HOH . J 6 HOH A 17 1017 3 HOH HOH . J 6 HOH A 18 1018 4 HOH HOH . J 6 HOH A 19 1019 161 HOH HOH . J 6 HOH A 20 1020 16 HOH HOH . J 6 HOH A 21 1021 5 HOH HOH . J 6 HOH A 22 1022 85 HOH HOH . J 6 HOH A 23 1023 72 HOH HOH . J 6 HOH A 24 1024 35 HOH HOH . J 6 HOH A 25 1025 79 HOH HOH . J 6 HOH A 26 1026 115 HOH HOH . J 6 HOH A 27 1027 12 HOH HOH . J 6 HOH A 28 1028 69 HOH HOH . J 6 HOH A 29 1029 44 HOH HOH . J 6 HOH A 30 1030 22 HOH HOH . J 6 HOH A 31 1031 67 HOH HOH . J 6 HOH A 32 1032 111 HOH HOH . J 6 HOH A 33 1033 51 HOH HOH . J 6 HOH A 34 1034 144 HOH HOH . J 6 HOH A 35 1035 57 HOH HOH . J 6 HOH A 36 1036 83 HOH HOH . J 6 HOH A 37 1037 137 HOH HOH . J 6 HOH A 38 1038 80 HOH HOH . J 6 HOH A 39 1039 39 HOH HOH . J 6 HOH A 40 1040 135 HOH HOH . J 6 HOH A 41 1041 10 HOH HOH . J 6 HOH A 42 1042 133 HOH HOH . J 6 HOH A 43 1043 123 HOH HOH . J 6 HOH A 44 1044 117 HOH HOH . J 6 HOH A 45 1045 54 HOH HOH . J 6 HOH A 46 1046 48 HOH HOH . J 6 HOH A 47 1047 122 HOH HOH . J 6 HOH A 48 1048 7 HOH HOH . J 6 HOH A 49 1049 20 HOH HOH . J 6 HOH A 50 1050 110 HOH HOH . J 6 HOH A 51 1051 78 HOH HOH . J 6 HOH A 52 1052 100 HOH HOH . J 6 HOH A 53 1053 21 HOH HOH . J 6 HOH A 54 1054 91 HOH HOH . J 6 HOH A 55 1055 94 HOH HOH . J 6 HOH A 56 1056 103 HOH HOH . J 6 HOH A 57 1057 154 HOH HOH . J 6 HOH A 58 1058 11 HOH HOH . J 6 HOH A 59 1059 143 HOH HOH . J 6 HOH A 60 1060 108 HOH HOH . J 6 HOH A 61 1061 126 HOH HOH . J 6 HOH A 62 1062 90 HOH HOH . J 6 HOH A 63 1063 41 HOH HOH . J 6 HOH A 64 1064 1 HOH HOH . J 6 HOH A 65 1065 96 HOH HOH . J 6 HOH A 66 1066 116 HOH HOH . J 6 HOH A 67 1067 32 HOH HOH . J 6 HOH A 68 1068 138 HOH HOH . J 6 HOH A 69 1069 145 HOH HOH . J 6 HOH A 70 1070 77 HOH HOH . J 6 HOH A 71 1071 132 HOH HOH . J 6 HOH A 72 1072 151 HOH HOH . J 6 HOH A 73 1073 159 HOH HOH . J 6 HOH A 74 1074 53 HOH HOH . J 6 HOH A 75 1075 98 HOH HOH . J 6 HOH A 76 1076 86 HOH HOH . J 6 HOH A 77 1077 163 HOH HOH . J 6 HOH A 78 1078 60 HOH HOH . J 6 HOH A 79 1079 118 HOH HOH . J 6 HOH A 80 1080 102 HOH HOH . J 6 HOH A 81 1081 152 HOH HOH . J 6 HOH A 82 1082 165 HOH HOH . J 6 HOH A 83 1083 153 HOH HOH . J 6 HOH A 84 1084 147 HOH HOH . J 6 HOH A 85 1085 158 HOH HOH . J 6 HOH A 86 1086 99 HOH HOH . J 6 HOH A 87 1087 36 HOH HOH . J 6 HOH A 88 1088 149 HOH HOH . J 6 HOH A 89 1089 73 HOH HOH . J 6 HOH A 90 1090 148 HOH HOH . J 6 HOH A 91 1091 84 HOH HOH . J 6 HOH A 92 1092 49 HOH HOH . J 6 HOH A 93 1093 124 HOH HOH . J 6 HOH A 94 1094 125 HOH HOH . K 6 HOH B 1 1001 56 HOH HOH . K 6 HOH B 2 1002 75 HOH HOH . K 6 HOH B 3 1003 68 HOH HOH . K 6 HOH B 4 1004 112 HOH HOH . K 6 HOH B 5 1005 63 HOH HOH . K 6 HOH B 6 1006 38 HOH HOH . K 6 HOH B 7 1007 101 HOH HOH . K 6 HOH B 8 1008 66 HOH HOH . K 6 HOH B 9 1009 47 HOH HOH . K 6 HOH B 10 1010 92 HOH HOH . K 6 HOH B 11 1011 114 HOH HOH . K 6 HOH B 12 1012 82 HOH HOH . K 6 HOH B 13 1013 37 HOH HOH . K 6 HOH B 14 1014 89 HOH HOH . K 6 HOH B 15 1015 139 HOH HOH . K 6 HOH B 16 1016 119 HOH HOH . K 6 HOH B 17 1017 120 HOH HOH . K 6 HOH B 18 1018 33 HOH HOH . K 6 HOH B 19 1019 87 HOH HOH . K 6 HOH B 20 1020 14 HOH HOH . K 6 HOH B 21 1021 18 HOH HOH . K 6 HOH B 22 1022 55 HOH HOH . K 6 HOH B 23 1023 81 HOH HOH . K 6 HOH B 24 1024 34 HOH HOH . K 6 HOH B 25 1025 93 HOH HOH . K 6 HOH B 26 1026 134 HOH HOH . K 6 HOH B 27 1027 29 HOH HOH . K 6 HOH B 28 1028 31 HOH HOH . K 6 HOH B 29 1029 43 HOH HOH . K 6 HOH B 30 1030 28 HOH HOH . K 6 HOH B 31 1031 40 HOH HOH . K 6 HOH B 32 1032 52 HOH HOH . K 6 HOH B 33 1033 76 HOH HOH . K 6 HOH B 34 1034 42 HOH HOH . K 6 HOH B 35 1035 109 HOH HOH . K 6 HOH B 36 1036 58 HOH HOH . K 6 HOH B 37 1037 97 HOH HOH . K 6 HOH B 38 1038 127 HOH HOH . K 6 HOH B 39 1039 17 HOH HOH . K 6 HOH B 40 1040 113 HOH HOH . K 6 HOH B 41 1041 70 HOH HOH . K 6 HOH B 42 1042 61 HOH HOH . K 6 HOH B 43 1043 50 HOH HOH . K 6 HOH B 44 1044 25 HOH HOH . K 6 HOH B 45 1045 15 HOH HOH . K 6 HOH B 46 1046 146 HOH HOH . K 6 HOH B 47 1047 65 HOH HOH . K 6 HOH B 48 1048 88 HOH HOH . K 6 HOH B 49 1049 62 HOH HOH . K 6 HOH B 50 1050 107 HOH HOH . K 6 HOH B 51 1051 23 HOH HOH . K 6 HOH B 52 1052 26 HOH HOH . K 6 HOH B 53 1053 46 HOH HOH . K 6 HOH B 54 1054 142 HOH HOH . K 6 HOH B 55 1055 157 HOH HOH . K 6 HOH B 56 1056 156 HOH HOH . K 6 HOH B 57 1057 121 HOH HOH . K 6 HOH B 58 1058 30 HOH HOH . K 6 HOH B 59 1059 141 HOH HOH . K 6 HOH B 60 1060 130 HOH HOH . K 6 HOH B 61 1061 74 HOH HOH . K 6 HOH B 62 1062 95 HOH HOH . K 6 HOH B 63 1063 162 HOH HOH . K 6 HOH B 64 1064 150 HOH HOH . K 6 HOH B 65 1065 166 HOH HOH . K 6 HOH B 66 1066 105 HOH HOH . K 6 HOH B 67 1067 164 HOH HOH . K 6 HOH B 68 1068 160 HOH HOH . K 6 HOH B 69 1069 136 HOH HOH . K 6 HOH B 70 1070 167 HOH HOH . K 6 HOH B 71 1071 140 HOH HOH . K 6 HOH B 72 1072 59 HOH HOH . K 6 HOH B 73 1073 129 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 C PR8 . . . C 2 -19.44 -19.473 -51.576 0.8 46.1 ? C PR8 901 A 1 HETATM 2 N N PR8 . . . C 2 -21.261 -19.899 -49.995 0.8 35.26 ? N PR8 901 A 1 HETATM 3 O O PR8 . . . C 2 -18.921 -20.502 -51.248 0.8 54.99 ? O PR8 901 A 1 HETATM 4 P P PR8 . . . C 2 -17.332 -18.643 -53.103 0.8 78.93 ? P PR8 901 A 1 HETATM 5 N N1 PR8 . . . C 2 -8.017 -19.025 -50.103 0.8 46.25 ? N1 PR8 901 A 1 HETATM 6 C C2 PR8 . . . C 2 -8.52 -17.891 -49.606 0.8 41.8 ? C2 PR8 901 A 1 HETATM 7 N N3 PR8 . . . C 2 -9.671 -17.283 -49.908 0.8 44.34 ? N3 PR8 901 A 1 HETATM 8 C C4 PR8 . . . C 2 -10.356 -17.968 -50.84 0.8 50.29 ? C4 PR8 901 A 1 HETATM 9 C C5 PR8 . . . C 2 -9.972 -19.164 -51.42 0.8 54.24 ? C5 PR8 901 A 1 HETATM 10 C C6 PR8 . . . C 2 -8.738 -19.711 -51.024 0.8 53.43 ? C6 PR8 901 A 1 HETATM 11 N N6 PR8 . . . C 2 -8.244 -20.865 -51.486 0.8 55.89 ? N6 PR8 901 A 1 HETATM 12 N N7 PR8 . . . C 2 -10.936 -19.586 -52.34 0.8 52.49 ? N7 PR8 901 A 1 HETATM 13 C C8 PR8 . . . C 2 -11.84 -18.637 -52.294 0.8 51.58 ? C8 PR8 901 A 1 HETATM 14 N N9 PR8 . . . C 2 -11.555 -17.629 -51.413 0.8 55.03 ? N9 PR8 901 A 1 HETATM 15 C CA PR8 . . . C 2 -20.762 -18.972 -51.021 0.8 35.81 ? CA PR8 901 A 1 HETATM 16 C CB PR8 . . . C 2 -20.671 -17.617 -50.314 0.8 34.8 ? CB PR8 901 A 1 HETATM 17 C CD PR8 . . . C 2 -21.112 -19.258 -48.678 0.8 34.85 ? CD PR8 901 A 1 HETATM 18 C CG PR8 . . . C 2 -20.344 -17.978 -48.9 0.8 34.58 ? CG PR8 901 A 1 HETATM 19 C C1' PR8 . . . C 2 -12.344 -16.436 -51.1 0.8 67.36 ? C1' PR8 901 A 1 HETATM 20 O O10 PR8 . . . C 2 -18.802 -18.725 -52.48 0.8 56.66 ? O10 PR8 901 A 1 HETATM 21 O O1P PR8 . . . C 2 -17.392 -18.004 -54.502 0.8 81.76 ? O1P PR8 901 A 1 HETATM 22 C C2' PR8 . . . C 2 -12.748 -15.534 -52.269 0.8 58.95 ? C2' PR8 901 A 1 HETATM 23 O O2' PR8 . . . C 2 -12.576 -14.168 -51.912 0.8 46.27 ? O2' PR8 901 A 1 HETATM 24 O O2P PR8 . . . C 2 -16.641 -19.946 -53.06 0.8 84.95 ? O2P PR8 901 A 1 HETATM 25 C C3' PR8 . . . C 2 -14.23 -15.864 -52.506 0.8 69.51 ? C3' PR8 901 A 1 HETATM 26 O O3' PR8 . . . C 2 -14.972 -14.672 -52.756 0.8 63.71 ? O3' PR8 901 A 1 HETATM 27 C C4' PR8 . . . C 2 -14.687 -16.575 -51.227 0.8 69.98 ? C4' PR8 901 A 1 HETATM 28 O O4' PR8 . . . C 2 -13.52 -16.825 -50.428 0.8 71.76 ? O4' PR8 901 A 1 HETATM 29 C C5' PR8 . . . C 2 -15.393 -17.89 -51.433 0.8 69.04 ? C5' PR8 901 A 1 HETATM 30 O O5' PR8 . . . C 2 -16.615 -17.63 -52.138 0.8 75.45 ? O5' PR8 901 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 30 #