data_8TWO # _model_server_result.job_id '_DInCTObXX3eeB5_KmAIgw' _model_server_result.datetime_utc '2024-11-27 07:35:46' _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 8two # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8TWO # _exptl.entry_id 8TWO _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 8TWO _cell.length_a 57.99 _cell.length_b 119.236 _cell.length_c 39.98 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TWO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 3 _struct_asym.id C _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 379 n n N1 C6 UDP sing 380 n n N1 C1' UDP sing 381 n n C2 N3 UDP sing 382 n n C2 O2 UDP doub 383 n n N3 C4 UDP sing 384 n n N3 HN3 UDP sing 385 n n C4 C5 UDP sing 386 n n C4 O4 UDP doub 387 n n C5 C6 UDP doub 388 n n C5 H5 UDP sing 389 n n C6 H6 UDP sing 390 n n C1' C2' UDP sing 391 n n C1' O4' UDP sing 392 n n C1' H1' UDP sing 393 n n C2' O2' UDP sing 394 n n C2' C3' UDP sing 395 n n C2' H2' UDP sing 396 n n O2' HO2' UDP sing 397 n n C3' C4' UDP sing 398 n n C3' O3' UDP sing 399 n n C3' H3' UDP sing 400 n n C4' O4' UDP sing 401 n n C4' C5' UDP sing 402 n n C4' H4' UDP sing 403 n n O3' HO3' UDP sing 404 n n C5' O5' UDP sing 405 n n C5' "H5'1" UDP sing 406 n n C5' "H5'2" UDP sing 407 n n O5' PA UDP sing 408 n n PA O1A UDP doub 409 n n PA O2A UDP sing 410 n n PA O3A UDP sing 411 n n O2A HOA2 UDP sing 412 n n O3A PB UDP sing 413 n n PB O1B UDP doub 414 n n PB O2B UDP sing 415 n n PB O3B UDP sing 416 n n O2B HOB2 UDP sing 417 n n O3B HOB3 UDP sing 418 n n # _atom_sites.entry_id 8TWO _atom_sites.fract_transf_matrix[1][1] 0.017244 _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] 0.008387 _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] 0.025013 _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 C 3 UDP A 1 401 1 UDP UDP . D 4 RAM A 1 402 1 RAM RAM . # 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 26.768 17.737 3.872 1 67.59 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . C 3 27.02 17.186 2.598 1 70.27 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . C 3 28.367 17.158 2.235 1 64.22 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . C 3 29.433 17.653 2.982 1 75.24 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . C 3 29.066 18.224 4.266 1 71.42 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . C 3 27.783 18.232 4.662 1 68.15 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . C 3 26.128 16.742 1.866 1 64.66 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . C 3 30.613 17.583 2.529 1 81.44 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . C 3 25.372 17.782 4.332 1 66.16 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . C 3 25.173 17.485 5.828 1 63.2 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . C 3 24.77 16.125 5.975 1 61.13 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . C 3 24.042 18.45 6.201 1 62.66 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . C 3 24.35 19.653 5.314 1 67.77 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . C 3 24.886 19.088 4.099 1 71.32 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . C 3 22.737 17.944 5.924 1 67.98 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . C 3 25.382 20.624 5.829 1 67.89 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . C 3 25.12 20.883 7.22 1 66.76 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . C 3 26.177 20.502 8.352 1 73.15 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . C 3 27.078 19.233 7.952 1 59.91 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . C 3 25.384 20.511 9.604 1 59.44 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . C 3 27.226 21.718 8.366 1 66.63 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . C 3 27.032 23.291 8.364 1 61.66 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . C 3 28.171 23.763 7.439 1 64.58 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . C 3 25.612 23.488 7.726 1 61.05 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . C 3 27.138 23.886 9.793 1 50.94 ? O3B UDP 401 A 1 HETATM 26 H HN3 UDP . . . C 3 28.565 16.834 1.457 1 77.19 ? HN3 UDP 401 A 1 HETATM 27 H H5 UDP . . . C 3 29.724 18.586 4.815 1 85.82 ? H5 UDP 401 A 1 HETATM 28 H H6 UDP . . . C 3 27.573 18.583 5.497 1 81.89 ? H6 UDP 401 A 1 HETATM 29 H H1' UDP . . . C 3 24.845 17.14 3.831 1 79.51 ? H1' UDP 401 A 1 HETATM 30 H H2' UDP . . . C 3 25.97 17.695 6.34 1 75.96 ? H2' UDP 401 A 1 HETATM 31 H HO2' UDP . . . C 3 23.985 15.999 5.661 1 73.48 ? HO2' UDP 401 A 1 HETATM 32 H H3' UDP . . . C 3 24.112 18.671 7.142 1 75.31 ? H3' UDP 401 A 1 HETATM 33 H H4' UDP . . . C 3 23.511 20.114 5.155 1 81.44 ? H4' UDP 401 A 1 HETATM 34 H HO3' UDP . . . C 3 22.627 17.872 5.085 1 81.69 ? HO3' UDP 401 A 1 HETATM 35 H "H5'1" UDP . . . C 3 26.269 20.242 5.731 1 81.58 ? "H5'1" UDP 401 A 1 HETATM 36 H "H5'2" UDP . . . C 3 25.331 21.453 5.329 1 81.58 ? "H5'2" UDP 401 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 461 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #