data_5JT0 # _model_server_result.job_id GsPqtJ4OislxNtfKulETzg _model_server_result.datetime_utc '2024-11-29 03:52:18' _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 5jt0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5JT0 # _exptl.entry_id 5JT0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 5JT0 _cell.length_a 98.734 _cell.length_b 98.734 _cell.length_c 127.589 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JT0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc3 B MN MN . A MN 401 1_555 C O3B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc4 B MN MN . A MN 401 1_555 G O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 367 n n N1 C6 UDP sing 368 n n N1 C1' UDP sing 369 n n C2 N3 UDP sing 370 n n C2 O2 UDP doub 371 n n N3 C4 UDP sing 372 n n N3 HN3 UDP sing 373 n n C4 C5 UDP sing 374 n n C4 O4 UDP doub 375 n n C5 C6 UDP doub 376 n n C5 H5 UDP sing 377 n n C6 H6 UDP sing 378 n n C1' C2' UDP sing 379 n n C1' O4' UDP sing 380 n n C1' H1' UDP sing 381 n n C2' O2' UDP sing 382 n n C2' C3' UDP sing 383 n n C2' H2' UDP sing 384 n n O2' HO2' UDP sing 385 n n C3' C4' UDP sing 386 n n C3' O3' UDP sing 387 n n C3' H3' UDP sing 388 n n C4' O4' UDP sing 389 n n C4' C5' UDP sing 390 n n C4' H4' UDP sing 391 n n O3' HO3' UDP sing 392 n n C5' O5' UDP sing 393 n n C5' "H5'1" UDP sing 394 n n C5' "H5'2" UDP sing 395 n n O5' PA UDP sing 396 n n PA O1A UDP doub 397 n n PA O2A UDP sing 398 n n PA O3A UDP sing 399 n n O2A HOA2 UDP sing 400 n n O3A PB UDP sing 401 n n PB O1B UDP doub 402 n n PB O2B UDP sing 403 n n PB O3B UDP sing 404 n n O2B HOB2 UDP sing 405 n n O3B HOB3 UDP sing 406 n n # _atom_sites.entry_id 5JT0 _atom_sites.fract_transf_matrix[1][1] 0.010128 _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] 0.010128 _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] 0.007838 _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 1 401 1 MN MN . C 3 UDP A 1 402 2 UDP UDP . D 4 EDO A 1 403 1 EDO EDO . E 4 EDO A 1 404 2 EDO EDO . F 5 XDX A 1 405 1 XDX XDX . G 6 HOH A 1 501 43 HOH HOH . G 6 HOH A 2 502 32 HOH HOH . G 6 HOH A 3 503 23 HOH HOH . G 6 HOH A 4 504 1 HOH HOH . G 6 HOH A 5 505 30 HOH HOH . G 6 HOH A 6 506 31 HOH HOH . G 6 HOH A 7 507 3 HOH HOH . G 6 HOH A 8 508 42 HOH HOH . G 6 HOH A 9 509 33 HOH HOH . G 6 HOH A 10 510 34 HOH HOH . G 6 HOH A 11 511 11 HOH HOH . G 6 HOH A 12 512 45 HOH HOH . G 6 HOH A 13 513 46 HOH HOH . G 6 HOH A 14 514 10 HOH HOH . G 6 HOH A 15 515 35 HOH HOH . G 6 HOH A 16 516 8 HOH HOH . G 6 HOH A 17 517 38 HOH HOH . G 6 HOH A 18 518 19 HOH HOH . G 6 HOH A 19 519 22 HOH HOH . G 6 HOH A 20 520 39 HOH HOH . G 6 HOH A 21 521 7 HOH HOH . G 6 HOH A 22 522 15 HOH HOH . G 6 HOH A 23 523 18 HOH HOH . G 6 HOH A 24 524 25 HOH HOH . G 6 HOH A 25 525 4 HOH HOH . G 6 HOH A 26 526 2 HOH HOH . G 6 HOH A 27 527 26 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 N N1 UDP . . . C 3 13.335 -14.969 -2.93 0.92 62.61 ? N1 UDP 402 A 1 HETATM 2 C C2 UDP . . . C 3 14.326 -15.676 -3.567 0.92 69.97 ? C2 UDP 402 A 1 HETATM 3 N N3 UDP . . . C 3 15.218 -14.931 -4.297 0.92 71.73 ? N3 UDP 402 A 1 HETATM 4 C C4 UDP . . . C 3 15.196 -13.556 -4.45 0.92 62.69 ? C4 UDP 402 A 1 HETATM 5 C C5 UDP . . . C 3 14.136 -12.877 -3.777 0.92 65.31 ? C5 UDP 402 A 1 HETATM 6 C C6 UDP . . . C 3 13.251 -13.592 -3.061 0.92 75.29 ? C6 UDP 402 A 1 HETATM 7 O O2 UDP . . . C 3 14.409 -16.9 -3.506 0.92 61.07 ? O2 UDP 402 A 1 HETATM 8 O O4 UDP . . . C 3 16.077 -13.014 -5.142 0.92 76.19 ? O4 UDP 402 A 1 HETATM 9 C C1' UDP . . . C 3 12.358 -15.703 -2.112 0.92 68.74 ? C1' UDP 402 A 1 HETATM 10 C C2' UDP . . . C 3 12.237 -15.192 -0.678 0.92 78.96 ? C2' UDP 402 A 1 HETATM 11 O O2' UDP . . . C 3 13.188 -15.849 0.152 0.92 78.41 ? O2' UDP 402 A 1 HETATM 12 C C3' UDP . . . C 3 10.802 -15.597 -0.324 0.92 81.21 ? C3' UDP 402 A 1 HETATM 13 C C4' UDP . . . C 3 10.07 -15.543 -1.67 0.92 81.84 ? C4' UDP 402 A 1 HETATM 14 O O4' UDP . . . C 3 11.085 -15.535 -2.697 0.92 83.67 ? O4' UDP 402 A 1 HETATM 15 O O3' UDP . . . C 3 10.758 -16.889 0.273 0.92 77.19 ? O3' UDP 402 A 1 HETATM 16 C C5' UDP . . . C 3 9.175 -14.346 -1.843 0.92 81.54 ? C5' UDP 402 A 1 HETATM 17 O O5' UDP . . . C 3 9.982 -13.166 -1.677 0.92 81.54 ? O5' UDP 402 A 1 HETATM 18 P PA UDP . . . C 3 9.492 -11.879 -0.878 0.92 88.8 ? PA UDP 402 A 1 HETATM 19 O O1A UDP . . . C 3 10.555 -10.801 -0.98 0.92 104.87 ? O1A UDP 402 A 1 HETATM 20 O O2A UDP . . . C 3 9.214 -12.178 0.538 0.92 119.18 ? O2A UDP 402 A 1 HETATM 21 O O3A UDP . . . C 3 8.131 -11.377 -1.543 0.92 107.96 ? O3A UDP 402 A 1 HETATM 22 P PB UDP . . . C 3 6.809 -10.915 -0.776 0.92 110.3 ? PB UDP 402 A 1 HETATM 23 O O1B UDP . . . C 3 6.062 -9.956 -1.684 0.92 109.79 ? O1B UDP 402 A 1 HETATM 24 O O2B UDP . . . C 3 7.167 -10.277 0.52 0.92 124.53 ? O2B UDP 402 A 1 HETATM 25 O O3B UDP . . . C 3 5.974 -12.171 -0.574 0.92 112.67 ? O3B UDP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 70 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #