data_3CL9 # _model_server_result.job_id K_Q8RI9lt6ISbjDgzvg5UQ _model_server_result.datetime_utc '2024-11-13 03:35:33' _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 3cl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":603}' # _entry.id 3CL9 # _exptl.entry_id 3CL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 3CL9 _cell.length_a 121.05 _cell.length_b 121.05 _cell.length_c 260.76 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CL9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L 1 1,2 A,B,C,D,E,F,G,H,I,J,K,L 2 1,3 A,B,C,D,E,F,G,H,I,J,K,L 3 1,2,4,3 # 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' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 508 n n N1 C6 UMP sing 509 n n N1 C1' UMP sing 510 n n C2 N3 UMP sing 511 n n C2 O2 UMP doub 512 n n N3 C4 UMP sing 513 n n N3 HN3 UMP sing 514 n n C4 C5 UMP sing 515 n n C4 O4 UMP doub 516 n n C5 C6 UMP doub 517 n n C5 H5 UMP sing 518 n n C6 H6 UMP sing 519 n n C1' C2' UMP sing 520 n n C1' O4' UMP sing 521 n n C1' H1' UMP sing 522 n n C2' C3' UMP sing 523 n n C2' H2' UMP sing 524 n n C2' "H2''" UMP sing 525 n n C3' C4' UMP sing 526 n n C3' O3' UMP sing 527 n n C3' H3' UMP sing 528 n n C4' O4' UMP sing 529 n n C4' C5' UMP sing 530 n n C4' H4' UMP sing 531 n n O3' HO3' UMP sing 532 n n C5' O5' UMP sing 533 n n C5' H5' UMP sing 534 n n C5' "H5''" UMP sing 535 n n O5' P UMP sing 536 n n P OP1 UMP doub 537 n n P OP2 UMP sing 538 n n P OP3 UMP sing 539 n n OP2 HOP2 UMP sing 540 n n OP3 HOP3 UMP sing 541 n n # _atom_sites.entry_id 3CL9 _atom_sites.fract_transf_matrix[1][1] 0.008261 _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] 0.008261 _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] 0.003835 _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 SO4 A 1 801 801 SO4 SO4 . C 2 SO4 A 1 802 802 SO4 SO4 . D 3 CL A 1 901 901 CL CL . E 3 CL A 1 902 902 CL CL . F 3 CL A 1 903 903 CL CL . G 4 NAP A 1 601 601 NAP NAP . H 5 MTX A 1 602 602 MTX MTX . I 6 UMP A 1 603 603 UMP UMP . J 7 EDO A 1 701 701 EDO EDO . K 7 EDO A 1 702 702 EDO EDO . L 8 HOH A 1 904 1 HOH HOH . L 8 HOH A 2 905 2 HOH HOH . L 8 HOH A 3 906 3 HOH HOH . L 8 HOH A 4 907 4 HOH HOH . L 8 HOH A 5 908 5 HOH HOH . L 8 HOH A 6 909 6 HOH HOH . L 8 HOH A 7 910 7 HOH HOH . L 8 HOH A 8 911 8 HOH HOH . L 8 HOH A 9 912 9 HOH HOH . L 8 HOH A 10 913 10 HOH HOH . L 8 HOH A 11 914 11 HOH HOH . L 8 HOH A 12 915 12 HOH HOH . L 8 HOH A 13 916 13 HOH HOH . L 8 HOH A 14 917 14 HOH HOH . L 8 HOH A 15 918 15 HOH HOH . L 8 HOH A 16 919 16 HOH HOH . L 8 HOH A 17 920 17 HOH HOH . L 8 HOH A 18 921 18 HOH HOH . L 8 HOH A 19 922 19 HOH HOH . L 8 HOH A 20 923 20 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 UMP . . . I 6 -11.309 -11.433 26.304 1 106.01 ? N1 UMP 603 A 1 HETATM 2 C C2 UMP . . . I 6 -11.291 -10.379 25.356 1 106.81 ? C2 UMP 603 A 1 HETATM 3 N N3 UMP . . . I 6 -11.784 -9.129 25.728 1 107.12 ? N3 UMP 603 A 1 HETATM 4 C C4 UMP . . . I 6 -12.292 -8.905 27.008 1 106.53 ? C4 UMP 603 A 1 HETATM 5 C C5 UMP . . . I 6 -12.317 -9.947 27.94 1 106.57 ? C5 UMP 603 A 1 HETATM 6 C C6 UMP . . . I 6 -11.828 -11.198 27.565 1 106.36 ? C6 UMP 603 A 1 HETATM 7 O O2 UMP . . . I 6 -10.855 -10.491 24.197 1 106.51 ? O2 UMP 603 A 1 HETATM 8 O O4 UMP . . . I 6 -12.722 -7.789 27.321 1 106.26 ? O4 UMP 603 A 1 HETATM 9 C C1' UMP . . . I 6 -10.819 -12.827 26.065 1 104.37 ? C1' UMP 603 A 1 HETATM 10 C C2' UMP . . . I 6 -9.667 -12.966 25.068 1 101.99 ? C2' UMP 603 A 1 HETATM 11 C C3' UMP . . . I 6 -8.739 -13.99 25.695 1 100.09 ? C3' UMP 603 A 1 HETATM 12 C C4' UMP . . . I 6 -9.065 -13.988 27.181 1 98.46 ? C4' UMP 603 A 1 HETATM 13 O O3' UMP . . . I 6 -8.999 -15.265 25.148 1 99.91 ? O3' UMP 603 A 1 HETATM 14 O O4' UMP . . . I 6 -10.337 -13.364 27.296 1 101.74 ? O4' UMP 603 A 1 HETATM 15 C C5' UMP . . . I 6 -8.008 -13.247 28.008 1 92.67 ? C5' UMP 603 A 1 HETATM 16 O O5' UMP . . . I 6 -7.715 -13.923 29.215 1 85.08 ? O5' UMP 603 A 1 HETATM 17 P P UMP . . . I 6 -6.323 -14.688 29.445 1 80.8 ? P UMP 603 A 1 HETATM 18 O OP1 UMP . . . I 6 -5.945 -15.346 28.153 1 81.35 ? OP1 UMP 603 A 1 HETATM 19 O OP2 UMP . . . I 6 -6.532 -15.711 30.518 1 81.03 ? OP2 UMP 603 A 1 HETATM 20 O OP3 UMP . . . I 6 -5.211 -13.816 29.859 1 80.23 ? OP3 UMP 603 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #