data_3LXO # _model_server_result.job_id FEnvHnU3gMJYaHidJnd5tA _model_server_result.datetime_utc '2024-11-14 18:53:31' _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 3lxo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 3LXO # _exptl.entry_id 3LXO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3'-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 120 _cell.entry_id 3LXO _cell.length_a 64.592 _cell.length_b 64.592 _cell.length_c 65.364 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LXO _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 PISA dimeric 2 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,B,C 1 1 A,B,C 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id T3P _chem_comp.mon_nstd_flag n _chem_comp.name "THYMIDINE-3'-PHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE" # 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 P OP1 T3P doub 290 n n P OP2 T3P sing 291 n n P OP3 T3P sing 292 n n P O3' T3P sing 293 n n OP2 HOP2 T3P sing 294 n n OP3 HOP3 T3P sing 295 n n O5' C5' T3P sing 296 n n O5' H5' T3P sing 297 n n C5' C4' T3P sing 298 n n C5' "H5'1" T3P sing 299 n n C5' "H5''" T3P sing 300 n n C4' O4' T3P sing 301 n n C4' C3' T3P sing 302 n n C4' H4' T3P sing 303 n n O4' C1' T3P sing 304 n n C3' O3' T3P sing 305 n n C3' C2' T3P sing 306 n n C3' H3' T3P sing 307 n n C2' C1' T3P sing 308 n n C2' H2' T3P sing 309 n n C2' "H2''" T3P sing 310 n n C1' N1 T3P sing 311 n n C1' H1' T3P sing 312 n n N1 C2 T3P sing 313 n n N1 C6 T3P sing 314 n n C2 O2 T3P doub 315 n n C2 N3 T3P sing 316 n n N3 C4 T3P sing 317 n n N3 H3 T3P sing 318 n n C4 O4 T3P doub 319 n n C4 C5 T3P sing 320 n n C5 C5M T3P sing 321 n n C5 C6 T3P doub 322 n n C5M H51 T3P sing 323 n n C5M H52 T3P sing 324 n n C5M H53 T3P sing 325 n n C6 H6 T3P sing 326 n n # _atom_sites.entry_id 3LXO _atom_sites.fract_transf_matrix[1][1] 0.015482 _atom_sites.fract_transf_matrix[1][2] 0.008938 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017877 _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] 0.015299 _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 B 2 T3P A 1 601 601 T3P T3P . C 3 HOH A 1 125 125 HOH HOH . C 3 HOH A 2 126 126 HOH HOH . C 3 HOH A 3 127 127 HOH HOH . C 3 HOH A 4 128 1 HOH HOH . C 3 HOH A 5 129 129 HOH HOH . C 3 HOH A 6 130 130 HOH HOH . C 3 HOH A 7 131 2 HOH HOH . C 3 HOH A 8 132 3 HOH HOH . C 3 HOH A 9 133 4 HOH HOH . C 3 HOH A 10 134 5 HOH HOH . C 3 HOH A 11 135 6 HOH HOH . C 3 HOH A 12 136 7 HOH HOH . C 3 HOH A 13 137 8 HOH HOH . C 3 HOH A 14 138 9 HOH HOH . C 3 HOH A 15 139 10 HOH HOH . C 3 HOH A 16 140 11 HOH HOH . C 3 HOH A 17 141 12 HOH HOH . C 3 HOH A 18 142 13 HOH HOH . C 3 HOH A 19 143 14 HOH HOH . C 3 HOH A 20 144 15 HOH HOH . C 3 HOH A 21 145 16 HOH HOH . C 3 HOH A 22 146 17 HOH HOH . C 3 HOH A 23 147 18 HOH HOH . C 3 HOH A 24 148 19 HOH HOH . C 3 HOH A 25 149 20 HOH HOH . C 3 HOH A 26 150 21 HOH HOH . C 3 HOH A 27 151 22 HOH HOH . C 3 HOH A 28 152 23 HOH HOH . C 3 HOH A 29 153 24 HOH HOH . C 3 HOH A 30 154 25 HOH HOH . C 3 HOH A 31 155 26 HOH HOH . C 3 HOH A 32 156 27 HOH HOH . C 3 HOH A 33 157 28 HOH HOH . C 3 HOH A 34 158 29 HOH HOH . C 3 HOH A 35 159 30 HOH HOH . C 3 HOH A 36 160 31 HOH HOH . C 3 HOH A 37 161 32 HOH HOH . C 3 HOH A 38 162 33 HOH HOH . C 3 HOH A 39 163 34 HOH HOH . C 3 HOH A 40 164 35 HOH HOH . C 3 HOH A 41 165 36 HOH HOH . C 3 HOH A 42 166 37 HOH HOH . C 3 HOH A 43 167 38 HOH HOH . C 3 HOH A 44 168 39 HOH HOH . C 3 HOH A 45 169 40 HOH HOH . C 3 HOH A 46 170 41 HOH HOH . C 3 HOH A 47 171 42 HOH HOH . C 3 HOH A 48 172 43 HOH HOH . C 3 HOH A 49 173 44 HOH HOH . C 3 HOH A 50 174 45 HOH HOH . C 3 HOH A 51 175 46 HOH HOH . C 3 HOH A 52 176 47 HOH HOH . C 3 HOH A 53 177 48 HOH HOH . C 3 HOH A 54 178 49 HOH HOH . C 3 HOH A 55 179 50 HOH HOH . C 3 HOH A 56 180 51 HOH HOH . C 3 HOH A 57 181 52 HOH HOH . C 3 HOH A 58 182 53 HOH HOH . C 3 HOH A 59 183 54 HOH HOH . C 3 HOH A 60 184 55 HOH HOH . C 3 HOH A 61 185 56 HOH HOH . C 3 HOH A 62 186 57 HOH HOH . C 3 HOH A 63 187 58 HOH HOH . C 3 HOH A 64 188 59 HOH HOH . C 3 HOH A 65 189 60 HOH HOH . C 3 HOH A 66 190 61 HOH HOH . C 3 HOH A 67 191 62 HOH HOH . C 3 HOH A 68 192 63 HOH HOH . C 3 HOH A 69 193 64 HOH HOH . C 3 HOH A 70 194 65 HOH HOH . C 3 HOH A 71 195 66 HOH HOH . C 3 HOH A 72 196 67 HOH HOH . C 3 HOH A 73 197 68 HOH HOH . C 3 HOH A 74 198 69 HOH HOH . C 3 HOH A 75 199 70 HOH HOH . C 3 HOH A 76 200 71 HOH HOH . C 3 HOH A 77 201 72 HOH HOH . C 3 HOH A 78 202 73 HOH HOH . C 3 HOH A 79 203 74 HOH HOH . C 3 HOH A 80 204 75 HOH HOH . C 3 HOH A 81 205 76 HOH HOH . C 3 HOH A 82 206 77 HOH HOH . C 3 HOH A 83 207 78 HOH HOH . C 3 HOH A 84 208 79 HOH HOH . C 3 HOH A 85 209 80 HOH HOH . C 3 HOH A 86 210 81 HOH HOH . C 3 HOH A 87 211 82 HOH HOH . C 3 HOH A 88 212 83 HOH HOH . C 3 HOH A 89 213 84 HOH HOH . C 3 HOH A 90 214 85 HOH HOH . C 3 HOH A 91 215 86 HOH HOH . C 3 HOH A 92 216 87 HOH HOH . C 3 HOH A 93 217 88 HOH HOH . C 3 HOH A 94 218 89 HOH HOH . C 3 HOH A 95 219 90 HOH HOH . C 3 HOH A 96 220 91 HOH HOH . C 3 HOH A 97 221 92 HOH HOH . C 3 HOH A 98 222 93 HOH HOH . C 3 HOH A 99 223 94 HOH HOH . C 3 HOH A 100 224 95 HOH HOH . C 3 HOH A 101 225 96 HOH HOH . C 3 HOH A 102 226 97 HOH HOH . C 3 HOH A 103 227 98 HOH HOH . C 3 HOH A 104 228 99 HOH HOH . C 3 HOH A 105 229 100 HOH HOH . C 3 HOH A 106 230 101 HOH HOH . C 3 HOH A 107 231 102 HOH HOH . C 3 HOH A 108 232 103 HOH HOH . C 3 HOH A 109 233 104 HOH HOH . C 3 HOH A 110 234 105 HOH HOH . C 3 HOH A 111 235 106 HOH HOH . C 3 HOH A 112 236 107 HOH HOH . C 3 HOH A 113 237 108 HOH HOH . C 3 HOH A 114 238 109 HOH HOH . C 3 HOH A 115 239 110 HOH HOH . C 3 HOH A 116 240 111 HOH HOH . C 3 HOH A 117 241 112 HOH HOH . C 3 HOH A 118 242 113 HOH HOH . C 3 HOH A 119 243 114 HOH HOH . C 3 HOH A 120 244 115 HOH HOH . C 3 HOH A 121 245 116 HOH HOH . C 3 HOH A 122 246 117 HOH HOH . C 3 HOH A 123 247 118 HOH HOH . C 3 HOH A 124 248 119 HOH HOH . C 3 HOH A 125 249 120 HOH HOH . C 3 HOH A 126 250 121 HOH HOH . C 3 HOH A 127 251 122 HOH HOH . C 3 HOH A 128 252 123 HOH HOH . C 3 HOH A 129 253 124 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 P P T3P . . . B 2 -2.291 -20.977 4.644 0.75 31.12 ? P T3P 601 A 1 HETATM 2 O OP1 T3P . . . B 2 -1.968 -20.12 3.458 0.75 38.78 ? OP1 T3P 601 A 1 HETATM 3 O OP2 T3P . . . B 2 -2.411 -22.407 4.193 0.75 23.66 ? OP2 T3P 601 A 1 HETATM 4 O OP3 T3P . . . B 2 -1.109 -20.812 5.63 0.75 55.79 ? OP3 T3P 601 A 1 HETATM 5 O O5' T3P . . . B 2 -4.215 -17.068 5.034 0.75 78.44 ? O5' T3P 601 A 1 HETATM 6 C C5' T3P . . . B 2 -5.474 -17.575 4.772 0.75 55.02 ? C5' T3P 601 A 1 HETATM 7 C C4' T3P . . . B 2 -5.677 -19.022 5.06 0.75 65.3 ? C4' T3P 601 A 1 HETATM 8 O O4' T3P . . . B 2 -6.952 -19.676 5.351 0.75 50.35 ? O4' T3P 601 A 1 HETATM 9 C C3' T3P . . . B 2 -4.689 -20.124 4.711 0.75 62.55 ? C3' T3P 601 A 1 HETATM 10 O O3' T3P . . . B 2 -3.56 -20.483 5.39 0.75 47.37 ? O3' T3P 601 A 1 HETATM 11 C C2' T3P . . . B 2 -5.559 -21.066 3.954 0.75 29.51 ? C2' T3P 601 A 1 HETATM 12 C C1' T3P . . . B 2 -6.823 -21.025 4.797 0.75 80.41 ? C1' T3P 601 A 1 HETATM 13 N N1 T3P . . . B 2 -8.035 -21.71 4.495 0.75 59.24 ? N1 T3P 601 A 1 HETATM 14 C C2 T3P . . . B 2 -8.198 -23.012 5.002 0.75 29.27 ? C2 T3P 601 A 1 HETATM 15 O O2 T3P . . . B 2 -7.305 -23.513 5.702 0.75 17.31 ? O2 T3P 601 A 1 HETATM 16 N N3 T3P . . . B 2 -9.351 -23.704 4.632 0.75 37.57 ? N3 T3P 601 A 1 HETATM 17 C C4 T3P . . . B 2 -10.242 -23.142 3.824 0.75 30.71 ? C4 T3P 601 A 1 HETATM 18 O O4 T3P . . . B 2 -11.385 -23.803 3.443 0.75 41.57 ? O4 T3P 601 A 1 HETATM 19 C C5 T3P . . . B 2 -10.052 -21.793 3.307 0.75 52.1 ? C5 T3P 601 A 1 HETATM 20 C C5M T3P . . . B 2 -11.09 -21.181 2.405 0.75 43.48 ? C5M T3P 601 A 1 HETATM 21 C C6 T3P . . . B 2 -8.935 -21.124 3.659 0.75 44.26 ? C6 T3P 601 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #