data_6KQX # _model_server_result.job_id CQ7riEma8FHdU9KAem93JA _model_server_result.datetime_utc '2025-02-05 15:53:10' _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 6kqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6KQX # _exptl.entry_id 6KQX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 6KQX _cell.length_a 52.152 _cell.length_b 116.722 _cell.length_c 185.226 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 6KQX _atom_sites.fract_transf_matrix[1][1] 0.019175 _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] 0.008567 _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] 0.005399 _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 UDP A 1 401 401 UDP UDP . C 3 HOH A 1 501 14 HOH HOH . C 3 HOH A 2 502 6 HOH HOH . C 3 HOH A 3 503 7 HOH HOH . C 3 HOH A 4 504 9 HOH HOH . C 3 HOH A 5 505 16 HOH HOH . C 3 HOH A 6 506 8 HOH HOH . C 3 HOH A 7 507 10 HOH HOH . C 3 HOH A 8 508 1 HOH HOH . C 3 HOH A 9 509 12 HOH HOH . C 3 HOH A 10 510 13 HOH HOH . C 3 HOH A 11 511 4 HOH HOH . C 3 HOH A 12 512 2 HOH HOH . C 3 HOH A 13 513 5 HOH HOH . C 3 HOH A 14 514 3 HOH HOH . C 3 HOH A 15 515 11 HOH HOH . C 3 HOH A 16 516 15 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 18 HOH HOH . C 3 HOH A 19 519 19 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 . . . B 2 -3.513 -12.564 -30.539 1 60.6 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 -3.291 -11.25 -30.905 1 67.75 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 -2.096 -11.018 -31.544 1 62.6 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 -1.122 -11.951 -31.845 1 62.05 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 -1.426 -13.288 -31.432 1 64.79 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 -2.588 -13.547 -30.804 1 61.68 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 -4.093 -10.353 -30.684 1 58.25 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 -0.088 -11.591 -32.431 1 64.69 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 -4.777 -12.874 -29.847 1 71.55 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 -5.871 -13.413 -30.768 1 51.66 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 -6.636 -12.355 -31.333 1 63.28 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 -6.695 -14.243 -29.786 1 68.44 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 -5.622 -14.834 -28.874 1 75.62 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 -4.528 -13.887 -28.889 1 72.18 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 -7.608 -13.439 -29.049 1 73.3 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 -5.118 -16.196 -29.279 1 60.99 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 -5.836 -17.208 -28.542 1 62.88 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 -6.279 -18.563 -29.228 1 62.87 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 -6.579 -18.355 -30.711 1 56.24 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 -7.364 -19.135 -28.395 1 57.39 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 -4.987 -19.49 -29.163 1 64.97 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 -4.013 -19.591 -27.916 1 57.41 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 -3.202 -20.854 -28.214 1 59.02 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 -3.13 -18.356 -28.074 1 55.53 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 -4.761 -19.649 -26.619 1 60.99 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #