data_5JUD # _model_server_result.job_id 8pqutZUulxOvL0l_WD_6yg _model_server_result.datetime_utc '2024-10-19 04:46:29' _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 5jud # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5JUD # _exptl.entry_id 5JUD _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 5JUD _cell.length_a 100.24 _cell.length_b 100.24 _cell.length_c 125.62 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JUD _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 _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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -100.24 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 5JUD _atom_sites.fract_transf_matrix[1][1] 0.009976 _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] 0.009976 _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] 0.007961 _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 1 UDP UDP . C 3 HOH A 1 501 35 HOH HOH . C 3 HOH A 2 502 34 HOH HOH . C 3 HOH A 3 503 24 HOH HOH . C 3 HOH A 4 504 5 HOH HOH . C 3 HOH A 5 505 36 HOH HOH . C 3 HOH A 6 506 28 HOH HOH . C 3 HOH A 7 507 8 HOH HOH . C 3 HOH A 8 508 38 HOH HOH . C 3 HOH A 9 509 2 HOH HOH . C 3 HOH A 10 510 6 HOH HOH . C 3 HOH A 11 511 4 HOH HOH . C 3 HOH A 12 512 30 HOH HOH . C 3 HOH A 13 513 9 HOH HOH . C 3 HOH A 14 514 20 HOH HOH . C 3 HOH A 15 515 49 HOH HOH . C 3 HOH A 16 516 22 HOH HOH . C 3 HOH A 17 517 7 HOH HOH . C 3 HOH A 18 518 23 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 12 HOH HOH . C 3 HOH A 21 521 16 HOH HOH . C 3 HOH A 22 522 29 HOH HOH . C 3 HOH A 23 523 10 HOH HOH . C 3 HOH A 24 524 48 HOH HOH . C 3 HOH A 25 525 11 HOH HOH . C 3 HOH A 26 526 32 HOH HOH . C 3 HOH A 27 527 25 HOH HOH . C 3 HOH A 28 528 45 HOH HOH . C 3 HOH A 29 529 14 HOH HOH . C 3 HOH A 30 530 15 HOH HOH . C 3 HOH A 31 531 26 HOH HOH . C 3 HOH A 32 532 27 HOH HOH . C 3 HOH A 33 533 18 HOH HOH . C 3 HOH A 34 534 47 HOH HOH . C 3 HOH A 35 535 41 HOH HOH . C 3 HOH A 36 536 50 HOH HOH . C 3 HOH A 37 537 40 HOH HOH . C 3 HOH A 38 538 39 HOH HOH . C 3 HOH A 39 539 42 HOH HOH . C 3 HOH A 40 540 43 HOH HOH . C 3 HOH A 41 541 33 HOH HOH . C 3 HOH A 42 542 21 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 13.448 -34.573 4.177 0.48 68.78 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 14.489 -34.006 4.774 0.48 64.42 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 15.351 -34.716 5.493 0.48 65.47 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 15.194 -36.039 5.641 0.48 65.31 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 14.108 -36.692 5.032 0.48 64.05 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 13.221 -35.893 4.283 0.48 71.61 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 14.664 -32.808 4.666 0.48 51.78 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 16.123 -36.779 6.409 0.48 63.92 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 12.596 -33.841 3.473 0.48 58.86 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 12.514 -34.341 1.992 0.48 68.06 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 13.503 -33.616 1.117 0.48 74.05 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 11.351 -34.171 1.608 0.48 76.94 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 10.426 -34.098 2.943 0.48 72.7 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 11.212 -34.114 3.955 0.48 76.66 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 11.215 -32.891 0.859 0.48 68.63 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 9.519 -35.296 2.981 0.48 76.37 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 10.34 -36.426 2.869 0.48 75.62 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 9.855 -37.626 1.95 0.48 71.72 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 10.752 -38.821 2.159 0.48 88.95 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 8.438 -37.973 2.33 0.48 82.05 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 9.937 -37.175 0.399 0.48 93.48 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 10.736 -37.984 -0.754 0.48 99.51 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 10.913 -37.079 -1.951 0.48 82.99 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 9.947 -39.219 -1.163 0.48 97.64 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 12.093 -38.392 -0.232 0.48 92.94 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 100 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #