data_5DBS # _model_server_result.job_id yUjr-leMLog1biH5212yPg _model_server_result.datetime_utc '2024-11-13 20:03:28' _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 5dbs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5DBS # _exptl.entry_id 5DBS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-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 5DBS _cell.length_a 90.39 _cell.length_b 90.39 _cell.length_c 133.293 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DBS _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 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 ? monomeric 1 author_defined_assembly 1 PISA tetrameric 4 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,D,E 1 1 A,B,C,D,E 2 1,2,3,4 # 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' 2_885 -x+3,-y+3,z -1 0 0 0 -1 0 0 0 1 271.17 271.17 0 3 'crystal symmetry operation' 3_855 -y+3,x,z 0 -1 0 1 0 0 0 0 1 271.17 0 0 4 'crystal symmetry operation' 4_585 y,-x+3,z 0 1 0 -1 0 0 0 0 1 0 271.17 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 A NE2 HIS 61 A HIS 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 A OD1 ASP 120 A ASP 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc4 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 B MN MN . A MN 301 1_555 D O3P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O1P TMP doub 310 n n P O2P TMP sing 311 n n P O3P TMP sing 312 n n P O5' TMP sing 313 n n O2P HOP2 TMP sing 314 n n O3P HOP3 TMP sing 315 n n O5' C5' TMP sing 316 n n C5' C4' TMP sing 317 n n C5' "H5'1" TMP sing 318 n n C5' "H5'2" TMP sing 319 n n C4' O4' TMP sing 320 n n C4' C3' TMP sing 321 n n C4' H4' TMP sing 322 n n O4' C1' TMP sing 323 n n C3' O3' TMP sing 324 n n C3' C2' TMP sing 325 n n C3' H3' TMP sing 326 n n O3' HO3' TMP sing 327 n n C2' C1' TMP sing 328 n n C2' "H2'1" TMP sing 329 n n C2' "H2'2" TMP sing 330 n n C1' N1 TMP sing 331 n n C1' H1' TMP sing 332 n n N1 C2 TMP sing 333 n n N1 C6 TMP sing 334 n n C2 O2 TMP doub 335 n n C2 N3 TMP sing 336 n n N3 C4 TMP sing 337 n n N3 HN3 TMP sing 338 n n C4 O4 TMP doub 339 n n C4 C5 TMP sing 340 n n C5 C5M TMP sing 341 n n C5 C6 TMP doub 342 n n C5M H51 TMP sing 343 n n C5M H52 TMP sing 344 n n C5M H53 TMP sing 345 n n C6 H6 TMP sing 346 n n # _atom_sites.entry_id 5DBS _atom_sites.fract_transf_matrix[1][1] 0.011063 _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] 0.011063 _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] 0.007502 _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 MN A 1 301 301 MN MN . C 3 SO4 A 1 302 1 SO4 SO4 . D 4 TMP A 1 303 1 TMP TMP . E 5 HOH A 1 401 11 HOH HOH . E 5 HOH A 2 402 13 HOH HOH . E 5 HOH A 3 403 17 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 18 HOH HOH . E 5 HOH A 6 406 2 HOH HOH . E 5 HOH A 7 407 15 HOH HOH . E 5 HOH A 8 408 6 HOH HOH . E 5 HOH A 9 409 14 HOH HOH . E 5 HOH A 10 410 4 HOH HOH . E 5 HOH A 11 411 9 HOH HOH . E 5 HOH A 12 412 12 HOH HOH . E 5 HOH A 13 413 16 HOH HOH . E 5 HOH A 14 414 1 HOH HOH . E 5 HOH A 15 415 10 HOH HOH . E 5 HOH A 16 416 3 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 TMP . . . D 4 128.102 105.876 419.062 1 70.99 ? P TMP 303 A 1 HETATM 2 O O1P TMP . . . D 4 126.747 106.641 419.141 1 54.93 ? O1P TMP 303 A 1 HETATM 3 O O2P TMP . . . D 4 128.08 104.382 419.347 1 72.49 ? O2P TMP 303 A 1 HETATM 4 O O3P TMP . . . D 4 129.387 106.549 419.515 1 64.31 ? O3P TMP 303 A 1 HETATM 5 O O5' TMP . . . D 4 128.384 105.808 417.453 1 65.92 ? O5' TMP 303 A 1 HETATM 6 C C5' TMP . . . D 4 129.66 105.554 416.845 1 66.75 ? C5' TMP 303 A 1 HETATM 7 C C4' TMP . . . D 4 129.332 105.53 415.341 1 66.07 ? C4' TMP 303 A 1 HETATM 8 O O4' TMP . . . D 4 128.31 104.56 415.033 1 64.91 ? O4' TMP 303 A 1 HETATM 9 C C3' TMP . . . D 4 128.759 106.87 414.874 1 62.67 ? C3' TMP 303 A 1 HETATM 10 O O3' TMP . . . D 4 129.29 107.211 413.603 1 70.25 ? O3' TMP 303 A 1 HETATM 11 C C2' TMP . . . D 4 127.266 106.704 414.739 1 62.23 ? C2' TMP 303 A 1 HETATM 12 C C1' TMP . . . D 4 127.196 105.219 414.397 1 65.32 ? C1' TMP 303 A 1 HETATM 13 N N1 TMP . . . D 4 125.884 104.597 414.655 1 73.64 ? N1 TMP 303 A 1 HETATM 14 C C2 TMP . . . D 4 125.296 103.778 413.62 1 79.44 ? C2 TMP 303 A 1 HETATM 15 O O2 TMP . . . D 4 125.874 103.582 412.519 1 78.89 ? O2 TMP 303 A 1 HETATM 16 N N3 TMP . . . D 4 124.093 103.186 413.795 1 83.33 ? N3 TMP 303 A 1 HETATM 17 C C4 TMP . . . D 4 123.407 103.323 414.94 1 84.42 ? C4 TMP 303 A 1 HETATM 18 O O4 TMP . . . D 4 122.297 102.754 415.056 1 90.71 ? O4 TMP 303 A 1 HETATM 19 C C5 TMP . . . D 4 123.982 104.156 416.043 1 80.37 ? C5 TMP 303 A 1 HETATM 20 C C5M TMP . . . D 4 123.242 104.342 417.343 1 83.36 ? C5M TMP 303 A 1 HETATM 21 C C6 TMP . . . D 4 125.228 104.757 415.838 1 76.7 ? C6 TMP 303 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 21 #