data_6AOG # _model_server_result.job_id klGeDYLCi0B-bUMzqLzZ-w _model_server_result.datetime_utc '2024-11-04 23:02:49' _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 6aog # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 6AOG # _exptl.entry_id 6AOG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 6AOG _cell.length_a 53.589 _cell.length_b 144.916 _cell.length_c 176.044 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AOG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 G N 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 529 n n N1 C6 UMP sing 530 n n N1 C1' UMP sing 531 n n C2 N3 UMP sing 532 n n C2 O2 UMP doub 533 n n N3 C4 UMP sing 534 n n N3 HN3 UMP sing 535 n n C4 C5 UMP sing 536 n n C4 O4 UMP doub 537 n n C5 C6 UMP doub 538 n n C5 H5 UMP sing 539 n n C6 H6 UMP sing 540 n n C1' C2' UMP sing 541 n n C1' O4' UMP sing 542 n n C1' H1' UMP sing 543 n n C2' C3' UMP sing 544 n n C2' H2' UMP sing 545 n n C2' "H2''" UMP sing 546 n n C3' C4' UMP sing 547 n n C3' O3' UMP sing 548 n n C3' H3' UMP sing 549 n n C4' O4' UMP sing 550 n n C4' C5' UMP sing 551 n n C4' H4' UMP sing 552 n n O3' HO3' UMP sing 553 n n C5' O5' UMP sing 554 n n C5' H5' UMP sing 555 n n C5' "H5''" UMP sing 556 n n O5' P UMP sing 557 n n P OP1 UMP doub 558 n n P OP2 UMP sing 559 n n P OP3 UMP sing 560 n n OP2 HOP2 UMP sing 561 n n OP3 HOP3 UMP sing 562 n n # _atom_sites.entry_id 6AOG _atom_sites.fract_transf_matrix[1][1] 0.018661 _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] 0.006901 _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] 0.00568 _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 2 UMP A 1 701 701 UMP UMP . D 3 NDP A 1 702 702 NDP NDP . E 4 CB3 A 1 703 703 CB3 CB3 . F 5 CP6 A 1 704 1 CP6 PYR . G 2 UMP B 1 701 701 UMP UMP . H 3 NDP B 1 702 702 NDP NDP . I 4 CB3 B 1 703 703 CB3 CB3 . J 5 CP6 B 1 704 2 CP6 PYR . # 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 . . . C 2 20.223 80.762 -33.829 1 69.88 ? N1 UMP 701 A 1 HETATM 2 C C2 UMP . . . C 2 20.969 80.704 -35.043 1 70.54 ? C2 UMP 701 A 1 HETATM 3 N N3 UMP . . . C 2 22.264 81.065 -35.05 1 71.43 ? N3 UMP 701 A 1 HETATM 4 C C4 UMP . . . C 2 22.876 81.489 -33.932 1 71.87 ? C4 UMP 701 A 1 HETATM 5 C C5 UMP . . . C 2 22.173 81.564 -32.732 1 71.65 ? C5 UMP 701 A 1 HETATM 6 C C6 UMP . . . C 2 20.83 81.197 -32.711 1 70.72 ? C6 UMP 701 A 1 HETATM 7 O O2 UMP . . . C 2 20.454 80.317 -36.119 1 69.49 ? O2 UMP 701 A 1 HETATM 8 O O4 UMP . . . C 2 24.081 81.821 -33.968 1 72.28 ? O4 UMP 701 A 1 HETATM 9 C C1' UMP . . . C 2 18.798 80.39 -33.752 1 68.91 ? C1' UMP 701 A 1 HETATM 10 C C2' UMP . . . C 2 18.485 78.994 -34.275 1 68.08 ? C2' UMP 701 A 1 HETATM 11 C C3' UMP . . . C 2 17.413 78.463 -33.344 1 66.63 ? C3' UMP 701 A 1 HETATM 12 C C4' UMP . . . C 2 17.467 79.336 -32.103 1 67.63 ? C4' UMP 701 A 1 HETATM 13 O O3' UMP . . . C 2 16.135 78.624 -33.958 1 64.27 ? O3' UMP 701 A 1 HETATM 14 O O4' UMP . . . C 2 18.359 80.414 -32.388 1 68.88 ? O4' UMP 701 A 1 HETATM 15 C C5' UMP . . . C 2 17.964 78.582 -30.876 1 67.47 ? C5' UMP 701 A 1 HETATM 16 O O5' UMP . . . C 2 16.958 77.677 -30.425 1 69.04 ? O5' UMP 701 A 1 HETATM 17 P P UMP . . . C 2 17.354 76.191 -29.946 1 69.94 ? P UMP 701 A 1 HETATM 18 O OP1 UMP . . . C 2 17.953 75.559 -31.179 1 69.79 ? OP1 UMP 701 A 1 HETATM 19 O OP2 UMP . . . C 2 16.041 75.585 -29.51 1 69.42 ? OP2 UMP 701 A 1 HETATM 20 O OP3 UMP . . . C 2 18.335 76.422 -28.824 1 69.83 ? OP3 UMP 701 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #