data_5JUC # _model_server_result.job_id 79tmvc3xclnDbG7AYSjC7Q _model_server_result.datetime_utc '2025-01-09 15:19:53' _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 5juc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5JUC # _exptl.entry_id 5JUC _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 5JUC _cell.length_a 99.434 _cell.length_b 99.434 _cell.length_c 126.785 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JUC _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 author_and_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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 99.434 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 metalc ? metalc1 A OD1 ASP 140 A ASP 136 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 E MN MN . A MN 404 1_555 G O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? # _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 5JUC _atom_sites.fract_transf_matrix[1][1] 0.010057 _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] 0.010057 _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] 0.007887 _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 EDO A 1 402 1 EDO EDO . D 3 EDO A 1 403 2 EDO EDO . E 4 MN A 1 404 1 MN MN . F 5 XDX A 1 405 1 XDX XDX . G 6 HOH A 1 501 31 HOH HOH . G 6 HOH A 2 502 15 HOH HOH . G 6 HOH A 3 503 32 HOH HOH . G 6 HOH A 4 504 2 HOH HOH . G 6 HOH A 5 505 22 HOH HOH . G 6 HOH A 6 506 9 HOH HOH . G 6 HOH A 7 507 7 HOH HOH . G 6 HOH A 8 508 4 HOH HOH . G 6 HOH A 9 509 1 HOH HOH . G 6 HOH A 10 510 26 HOH HOH . G 6 HOH A 11 511 34 HOH HOH . G 6 HOH A 12 512 10 HOH HOH . G 6 HOH A 13 513 12 HOH HOH . G 6 HOH A 14 514 17 HOH HOH . G 6 HOH A 15 515 29 HOH HOH . G 6 HOH A 16 516 20 HOH HOH . G 6 HOH A 17 517 13 HOH HOH . G 6 HOH A 18 518 28 HOH HOH . G 6 HOH A 19 519 5 HOH HOH . G 6 HOH A 20 520 21 HOH HOH . G 6 HOH A 21 521 23 HOH HOH . G 6 HOH A 22 522 33 HOH HOH . G 6 HOH A 23 523 3 HOH HOH . G 6 HOH A 24 524 8 HOH HOH . G 6 HOH A 25 525 27 HOH HOH . G 6 HOH A 26 526 19 HOH HOH . G 6 HOH A 27 527 16 HOH HOH . G 6 HOH A 28 528 25 HOH HOH . G 6 HOH A 29 529 18 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 34.706 -13.395 26.236 1 63.85 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 33.96 -14.42 25.696 1 62.91 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 34.655 -15.303 24.902 1 61.92 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 36.006 -15.268 24.626 1 60.45 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 36.718 -14.181 25.22 1 61.57 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 36.06 -13.297 25.99 1 62.1 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 32.762 -14.563 25.925 1 59.17 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 36.511 -16.168 23.935 1 64 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 34.011 -12.386 27.052 1 63.69 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 34.402 -12.409 28.527 1 69.97 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 33.595 -13.32 29.266 1 66.26 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 34.11 -10.963 28.944 1 73.14 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 34.383 -10.161 27.667 1 69.65 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 34.378 -11.108 26.575 1 69.38 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 32.758 -10.811 29.354 1 64.81 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 35.674 -9.381 27.653 1 71.94 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 36.77 -10.291 27.878 1 74.36 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 38.096 -9.957 28.696 1 100.49 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 38.644 -8.626 28.329 1 89.93 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 39.111 -11.065 28.41 1 85.03 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 37.787 -10.021 30.259 1 106.96 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 38.077 -11.106 31.393 1 102.06 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 38.678 -12.348 30.703 1 114.88 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 36.847 -11.443 32.158 1 81.95 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 39.132 -10.494 32.295 1 102.26 ? 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 325 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #