data_8WP5 # _model_server_result.job_id hZgyA7OpRRJkp7NVjZIbCg _model_server_result.datetime_utc '2024-10-11 04:25:33' _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 8wp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8WP5 # _exptl.entry_id 8WP5 _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 8WP5 _cell.length_a 122.24 _cell.length_b 122.24 _cell.length_c 81.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WP5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall 'P 4nw 2abw' _symmetry.space_group_name_H-M 'P 43 21 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,D _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 311 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 301 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 311 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 7_555 _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 2.032 _struct_conn.pdbx_value_order ? # _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 8WP5 _atom_sites.fract_transf_matrix[1][1] 0.008181 _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] 0.008181 _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] 0.012267 _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 1 501 1 UDP UDP . C 3 CL A 1 502 1 CL CL . D 4 HOH A 1 601 19 HOH HOH . D 4 HOH A 2 602 13 HOH HOH . D 4 HOH A 3 603 18 HOH HOH . D 4 HOH A 4 604 2 HOH HOH . D 4 HOH A 5 605 14 HOH HOH . D 4 HOH A 6 606 17 HOH HOH . D 4 HOH A 7 607 4 HOH HOH . D 4 HOH A 8 608 24 HOH HOH . D 4 HOH A 9 609 8 HOH HOH . D 4 HOH A 10 610 1 HOH HOH . D 4 HOH A 11 611 15 HOH HOH . D 4 HOH A 12 612 16 HOH HOH . D 4 HOH A 13 613 12 HOH HOH . D 4 HOH A 14 614 11 HOH HOH . D 4 HOH A 15 615 20 HOH HOH . D 4 HOH A 16 616 23 HOH HOH . D 4 HOH A 17 617 21 HOH HOH . D 4 HOH A 18 618 10 HOH HOH . D 4 HOH A 19 619 22 HOH HOH . D 4 HOH A 20 620 5 HOH HOH . D 4 HOH A 21 621 7 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 8.045 31.076 -22.028 1 74.31 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 9.24 30.698 -22.616 1 72.16 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 10.317 30.652 -21.765 1 67.24 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 10.317 30.933 -20.413 1 64.58 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 9.044 31.31 -19.878 1 69.89 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 7.97 31.367 -20.685 1 68.24 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 9.342 30.433 -23.805 1 69.13 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 11.375 30.847 -19.77 1 57.78 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 6.849 31.144 -22.884 1 71.53 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 6.045 29.842 -22.887 1 66.65 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 6.414 29.056 -24.014 1 63.51 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 4.599 30.335 -23.005 1 63.48 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 4.632 31.706 -22.329 1 67.45 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 6.003 32.159 -22.382 1 66.16 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 4.147 30.413 -24.353 1 58.74 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 4.143 31.74 -20.903 1 66.87 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 2.763 31.319 -20.852 1 60.69 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 1.844 31.674 -19.614 1 46.03 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 2.482 31.08 -18.417 1 57.16 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 0.391 31.29 -19.874 1 63.99 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 1.877 33.267 -19.534 1 73.45 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 2.347 34.127 -18.29 1 78.34 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 1.794 33.343 -17.098 1 75.2 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 3.874 34.017 -18.351 1 66.68 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 1.84 35.532 -18.353 1 83.86 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #