data_6OJV # _model_server_result.job_id 0sh8HfLKAY1EhsNfQ5g0Yw _model_server_result.datetime_utc '2024-11-15 04:16:03' _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 6ojv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":600}' # _entry.id 6OJV # _exptl.entry_id 6OJV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 128.92 _cell.angle_gamma 90 _cell.entry_id 6OJV _cell.length_a 154.95 _cell.length_b 103.033 _cell.length_c 109.211 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OJV _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,I,J,M,O 1 1 B,D,G,H,K,L,N,P 2 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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 409 n n N1 C6 UMP sing 410 n n N1 C1' UMP sing 411 n n C2 N3 UMP sing 412 n n C2 O2 UMP doub 413 n n N3 C4 UMP sing 414 n n N3 HN3 UMP sing 415 n n C4 C5 UMP sing 416 n n C4 O4 UMP doub 417 n n C5 C6 UMP doub 418 n n C5 H5 UMP sing 419 n n C6 H6 UMP sing 420 n n C1' C2' UMP sing 421 n n C1' O4' UMP sing 422 n n C1' H1' UMP sing 423 n n C2' C3' UMP sing 424 n n C2' H2' UMP sing 425 n n C2' "H2''" UMP sing 426 n n C3' C4' UMP sing 427 n n C3' O3' UMP sing 428 n n C3' H3' UMP sing 429 n n C4' O4' UMP sing 430 n n C4' C5' UMP sing 431 n n C4' H4' UMP sing 432 n n O3' HO3' UMP sing 433 n n C5' O5' UMP sing 434 n n C5' H5' UMP sing 435 n n C5' "H5''" UMP sing 436 n n O5' P UMP sing 437 n n P OP1 UMP doub 438 n n P OP2 UMP sing 439 n n P OP3 UMP sing 440 n n OP2 HOP2 UMP sing 441 n n OP3 HOP3 UMP sing 442 n n # _atom_sites.entry_id 6OJV _atom_sites.fract_transf_matrix[1][1] 0.006454 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005211 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009706 _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] 0.011769 _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 E 2 UMP B 1 600 600 UMP UMP . F 3 2XB B 1 601 601 2XB 906 . G 2 UMP A 1 600 600 UMP UMP . H 3 2XB A 1 601 601 2XB 906 . I 2 UMP C 1 600 600 UMP UMP . J 3 2XB C 1 601 601 2XB 906 . K 2 UMP D 1 600 600 UMP UMP . L 3 2XB D 1 601 601 2XB 906 . M 4 HOH B 1 701 16 HOH HOH . M 4 HOH B 2 702 14 HOH HOH . M 4 HOH B 3 703 18 HOH HOH . M 4 HOH B 4 704 26 HOH HOH . M 4 HOH B 5 705 21 HOH HOH . M 4 HOH B 6 706 28 HOH HOH . M 4 HOH B 7 707 19 HOH HOH . M 4 HOH B 8 708 5 HOH HOH . M 4 HOH B 9 709 10 HOH HOH . M 4 HOH B 10 710 9 HOH HOH . M 4 HOH B 11 711 3 HOH HOH . M 4 HOH B 12 712 13 HOH HOH . M 4 HOH B 13 713 37 HOH HOH . N 4 HOH A 1 701 34 HOH HOH . N 4 HOH A 2 702 23 HOH HOH . N 4 HOH A 3 703 8 HOH HOH . N 4 HOH A 4 704 22 HOH HOH . N 4 HOH A 5 705 6 HOH HOH . N 4 HOH A 6 706 11 HOH HOH . O 4 HOH C 1 701 4 HOH HOH . O 4 HOH C 2 702 30 HOH HOH . O 4 HOH C 3 703 2 HOH HOH . O 4 HOH C 4 704 36 HOH HOH . O 4 HOH C 5 705 20 HOH HOH . O 4 HOH C 6 706 1 HOH HOH . O 4 HOH C 7 707 24 HOH HOH . P 4 HOH D 1 701 27 HOH HOH . P 4 HOH D 2 702 33 HOH HOH . P 4 HOH D 3 703 29 HOH HOH . P 4 HOH D 4 704 31 HOH HOH . P 4 HOH D 5 705 35 HOH HOH . P 4 HOH D 6 706 38 HOH HOH . P 4 HOH D 7 707 17 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 . . . E 2 121.63 34.766 261.76 1 63.16 ? N1 UMP 600 B 1 HETATM 2 C C2 UMP . . . E 2 122.051 34.512 263.087 1 61.41 ? C2 UMP 600 B 1 HETATM 3 N N3 UMP . . . E 2 123.247 33.811 263.248 1 60.18 ? N3 UMP 600 B 1 HETATM 4 C C4 UMP . . . E 2 124.061 33.336 262.218 1 63.62 ? C4 UMP 600 B 1 HETATM 5 C C5 UMP . . . E 2 123.573 33.624 260.878 1 61.25 ? C5 UMP 600 B 1 HETATM 6 C C6 UMP . . . E 2 122.41 34.293 260.711 1 65.08 ? C6 UMP 600 B 1 HETATM 7 O O2 UMP . . . E 2 121.427 34.876 264.083 1 61.65 ? O2 UMP 600 B 1 HETATM 8 O O4 UMP . . . E 2 125.095 32.727 262.479 1 68.21 ? O4 UMP 600 B 1 HETATM 9 C C1' UMP . . . E 2 120.349 35.519 261.464 1 60.3 ? C1' UMP 600 B 1 HETATM 10 C C2' UMP . . . E 2 120.266 36.918 262.078 1 61.99 ? C2' UMP 600 B 1 HETATM 11 C C3' UMP . . . E 2 119.237 37.549 261.158 1 63.17 ? C3' UMP 600 B 1 HETATM 12 C C4' UMP . . . E 2 119.546 36.919 259.795 1 58.38 ? C4' UMP 600 B 1 HETATM 13 O O3' UMP . . . E 2 117.927 37.245 261.593 1 66.35 ? O3' UMP 600 B 1 HETATM 14 O O4' UMP . . . E 2 120.268 35.724 260.091 1 62.07 ? O4' UMP 600 B 1 HETATM 15 C C5' UMP . . . E 2 120.384 37.825 258.879 1 59.29 ? C5' UMP 600 B 1 HETATM 16 O O5' UMP . . . E 2 119.63 38.858 258.267 1 64.58 ? O5' UMP 600 B 1 HETATM 17 P P UMP . . . E 2 120.165 40.393 258.157 1 63.24 ? P UMP 600 B 1 HETATM 18 O OP1 UMP . . . E 2 121.304 40.64 257.228 1 62.87 ? OP1 UMP 600 B 1 HETATM 19 O OP2 UMP . . . E 2 118.797 41.181 257.79 1 63.23 -1 OP2 UMP 600 B 1 HETATM 20 O OP3 UMP . . . E 2 120.416 40.796 259.709 1 54.58 -1 OP3 UMP 600 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #