data_3ROG # _model_server_result.job_id 9iGZq21nKM4yWmFmCU9FsQ _model_server_result.datetime_utc '2024-12-04 11:31:54' _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 3rog # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":265}' # _entry.id 3ROG # _exptl.entry_id 3ROG _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 3ROG _cell.length_a 126.094 _cell.length_b 126.094 _cell.length_c 110.962 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ROG _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 dimeric 2 software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1,2 A,B,C,D 2 1,3 A,B,C,D 3 1,4,5,3,6,7 # 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' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 63.047 36.400202 36.987333 3 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 6_555 -x,-x+y,-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 covale ? covale1 A C LEU 54 A LEU 53 1_555 A N MSE 55 A MSE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale2 A C MSE 55 A MSE 54 1_555 A N GLU 56 A GLU 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale3 A C SER 74 A SER 73 1_555 A N MSE 75 A MSE 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C MSE 75 A MSE 74 1_555 A N SER 76 A SER 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale5 A C LYS 131 A LYS 130 1_555 A N MSE 132 A MSE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale6 A C MSE 132 A MSE 131 1_555 A N ASP 133 A ASP 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C GLU 139 A GLU 138 1_555 A N MSE 140 A MSE 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale8 A C MSE 140 A MSE 139 1_555 A N PRO 141 A PRO 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale9 A C PRO 144 A PRO 143 1_555 A N MSE 145 A MSE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale10 A C MSE 145 A MSE 144 1_555 A N MSE 146 A MSE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale11 A C MSE 146 A MSE 145 1_555 A N VAL 147 A VAL 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? # _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 294 n n P OP2 T3P sing 295 n n P OP3 T3P sing 296 n n P O3' T3P sing 297 n n OP2 HOP2 T3P sing 298 n n OP3 HOP3 T3P sing 299 n n O5' C5' T3P sing 300 n n O5' H5' T3P sing 301 n n C5' C4' T3P sing 302 n n C5' "H5'1" T3P sing 303 n n C5' "H5''" T3P sing 304 n n C4' O4' T3P sing 305 n n C4' C3' T3P sing 306 n n C4' H4' T3P sing 307 n n O4' C1' T3P sing 308 n n C3' O3' T3P sing 309 n n C3' C2' T3P sing 310 n n C3' H3' T3P sing 311 n n C2' C1' T3P sing 312 n n C2' H2' T3P sing 313 n n C2' "H2''" T3P sing 314 n n C1' N1 T3P sing 315 n n C1' H1' T3P sing 316 n n N1 C2 T3P sing 317 n n N1 C6 T3P sing 318 n n C2 O2 T3P doub 319 n n C2 N3 T3P sing 320 n n N3 C4 T3P sing 321 n n N3 H3 T3P sing 322 n n C4 O4 T3P doub 323 n n C4 C5 T3P sing 324 n n C5 C5M T3P sing 325 n n C5 C6 T3P doub 326 n n C5M H51 T3P sing 327 n n C5M H52 T3P sing 328 n n C5M H53 T3P sing 329 n n C6 H6 T3P sing 330 n n # _atom_sites.entry_id 3ROG _atom_sites.fract_transf_matrix[1][1] 0.007931 _atom_sites.fract_transf_matrix[1][2] 0.004579 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009157 _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] 0.009012 _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 1 265 1 T3P T3P . C 3 SO4 A 1 266 2 SO4 SO4 . D 4 HOH A 1 267 1 HOH HOH . D 4 HOH A 2 268 2 HOH HOH . D 4 HOH A 3 269 3 HOH HOH . D 4 HOH A 4 270 4 HOH HOH . D 4 HOH A 5 271 5 HOH HOH . D 4 HOH A 6 272 6 HOH HOH . D 4 HOH A 7 273 7 HOH HOH . D 4 HOH A 8 274 8 HOH HOH . D 4 HOH A 9 275 9 HOH HOH . D 4 HOH A 10 276 10 HOH HOH . D 4 HOH A 11 277 11 HOH HOH . D 4 HOH A 12 278 12 HOH HOH . D 4 HOH A 13 279 13 HOH HOH . D 4 HOH A 14 280 14 HOH HOH . D 4 HOH A 15 281 15 HOH HOH . D 4 HOH A 16 282 16 HOH HOH . D 4 HOH A 17 283 17 HOH HOH . D 4 HOH A 18 284 18 HOH HOH . D 4 HOH A 19 285 19 HOH HOH . D 4 HOH A 20 286 20 HOH HOH . D 4 HOH A 21 287 21 HOH HOH . D 4 HOH A 22 288 22 HOH HOH . D 4 HOH A 23 289 23 HOH HOH . D 4 HOH A 24 290 24 HOH HOH . D 4 HOH A 25 291 25 HOH HOH . D 4 HOH A 26 292 26 HOH HOH . D 4 HOH A 27 293 27 HOH HOH . D 4 HOH A 28 294 28 HOH HOH . D 4 HOH A 29 295 29 HOH HOH . D 4 HOH A 30 296 30 HOH HOH . D 4 HOH A 31 297 31 HOH HOH . D 4 HOH A 32 298 32 HOH HOH . D 4 HOH A 33 299 33 HOH HOH . D 4 HOH A 34 300 34 HOH HOH . D 4 HOH A 35 301 35 HOH HOH . D 4 HOH A 36 302 36 HOH HOH . D 4 HOH A 37 303 37 HOH HOH . D 4 HOH A 38 304 38 HOH HOH . D 4 HOH A 39 305 39 HOH HOH . D 4 HOH A 40 306 40 HOH HOH . D 4 HOH A 41 307 41 HOH HOH . D 4 HOH A 42 308 42 HOH HOH . D 4 HOH A 43 309 43 HOH HOH . D 4 HOH A 44 310 44 HOH HOH . D 4 HOH A 45 311 45 HOH HOH . D 4 HOH A 46 312 46 HOH HOH . D 4 HOH A 47 313 47 HOH HOH . D 4 HOH A 48 314 48 HOH HOH . D 4 HOH A 49 315 49 HOH HOH . D 4 HOH A 50 316 50 HOH HOH . D 4 HOH A 51 317 51 HOH HOH . D 4 HOH A 52 318 52 HOH HOH . D 4 HOH A 53 319 53 HOH HOH . D 4 HOH A 54 320 54 HOH HOH . D 4 HOH A 55 321 55 HOH HOH . D 4 HOH A 56 322 56 HOH HOH . D 4 HOH A 57 323 57 HOH HOH . D 4 HOH A 58 324 58 HOH HOH . D 4 HOH A 59 325 59 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 16.222 25.402 23.354 1 66.81 ? P T3P 265 A 1 HETATM 2 O OP1 T3P . . . B 2 15.517 24.055 23.327 1 65.54 ? OP1 T3P 265 A 1 HETATM 3 O OP2 T3P . . . B 2 16.742 25.839 21.994 1 68.24 ? OP2 T3P 265 A 1 HETATM 4 O OP3 T3P . . . B 2 15.507 26.539 24.063 1 68.73 ? OP3 T3P 265 A 1 HETATM 5 O O5' T3P . . . B 2 17.845 25.779 28.646 1 63.65 ? O5' T3P 265 A 1 HETATM 6 C C5' T3P . . . B 2 18.97 25.584 27.766 1 64.98 ? C5' T3P 265 A 1 HETATM 7 C C4' T3P . . . B 2 18.672 24.884 26.428 1 63.43 ? C4' T3P 265 A 1 HETATM 8 O O4' T3P . . . B 2 18.497 23.479 26.598 1 62.51 ? O4' T3P 265 A 1 HETATM 9 C C3' T3P . . . B 2 17.401 25.361 25.754 1 64.76 ? C3' T3P 265 A 1 HETATM 10 O O3' T3P . . . B 2 17.484 25.097 24.336 1 65.55 ? O3' T3P 265 A 1 HETATM 11 C C2' T3P . . . B 2 16.345 24.487 26.372 1 63.33 ? C2' T3P 265 A 1 HETATM 12 C C1' T3P . . . B 2 17.099 23.188 26.527 1 63.4 ? C1' T3P 265 A 1 HETATM 13 N N1 T3P . . . B 2 16.65 22.459 27.721 1 65.05 ? N1 T3P 265 A 1 HETATM 14 C C2 T3P . . . B 2 15.85 21.327 27.488 1 65.13 ? C2 T3P 265 A 1 HETATM 15 O O2 T3P . . . B 2 15.561 21.051 26.316 1 60.38 ? O2 T3P 265 A 1 HETATM 16 N N3 T3P . . . B 2 15.394 20.577 28.507 1 66.26 ? N3 T3P 265 A 1 HETATM 17 C C4 T3P . . . B 2 15.67 20.873 29.799 1 65.88 ? C4 T3P 265 A 1 HETATM 18 O O4 T3P . . . B 2 15.216 20.12 30.711 1 64.98 ? O4 T3P 265 A 1 HETATM 19 C C5 T3P . . . B 2 16.531 22.069 30.101 1 66.87 ? C5 T3P 265 A 1 HETATM 20 C C5M T3P . . . B 2 16.895 22.48 31.527 1 58.68 ? C5M T3P 265 A 1 HETATM 21 C C6 T3P . . . B 2 16.982 22.817 28.988 1 65.59 ? C6 T3P 265 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #